Variant report

Variant	rs12949078
Chromosome Location	chr17:18215586-18215587
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF3	chr17:18215514-18215700	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:18215429-18215729	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:18215543-18215593	Hepatocyte	liver:	n/a
2	chr17:18215543-18215593	HCT-116	colon:	n/a
3	chr17:18215543-18215593	IMR90	lung:	fetal
4	chr17:18215543-18215593	NB4	blood:	n/a
5	chr17:18215543-18215593	HL-60	blood:	n/a
6	chr17:18215543-18215593	HCM	heart:	n/a
7	chr17:18215543-18215593	GM12891	blood:	n/a
8	chr17:18215543-18215593	Caco-2	colon:	n/a
9	chr17:18215543-18215593	NHDF-neo	bronchial:	n/a
10	chr17:18215543-18215593	HAEpiC	amniotic membrane:	n/a
11	chr17:18215543-18215593	HNPCEpiC	eye:	n/a
12	chr17:18215543-18215593	U87	brain:	n/a
13	chr17:18215543-18215593	Hela-S3	cervix:	n/a
14	chr17:18215543-18215593	HEK293	kidney:	embryo
15	chr17:18215543-18215593	HEEpiC	esophagus:	n/a
16	chr17:18215543-18215593	ProgFib	skin:	n/a
17	chr17:18215543-18215593	GM19239	blood:	n/a
18	chr17:18215543-18215593	HCPEpiC	choroid plexus:	n/a
19	chr17:18215543-18215593	AoSMC	blood vessel:	n/a
20	chr17:18215543-18215593	HIPEpiC	eye:	n/a
21	chr17:18215543-18215593	A549	lung:	n/a
22	chr17:18215543-18215593	AG10803	skin:	n/a
23	chr17:18215543-18215593	SK-N-MC	brain:	n/a
24	chr17:18215543-18215593	AG09319	gingival:	n/a
25	chr17:18215543-18215593	BJ	skin:	n/a
26	chr17:18215543-18215593	HRE	kidney:	n/a
27	chr17:18215543-18215593	SAEC	small airway:	n/a
28	chr17:18215543-18215593	SK-N-SH_RA	brain:	n/a
29	chr17:18215543-18215593	K562	blood:	n/a
30	chr17:18215543-18215593	ECC-1	luminal epithelium:	n/a
31	chr17:18215543-18215593	NH-A	brain:	n/a
32	chr17:18215543-18215593	AG04450	lung:	fetal
33	chr17:18215543-18215593	HRCEpiC	kidney:	n/a
34	chr17:18215543-18215593	GM06990	blood:	n/a
35	chr17:18215543-18215593	HMEC	breast:	n/a
36	chr17:18215543-18215593	SK-N-SH	brain:	n/a
37	chr17:18215543-18215593	RPTEC	kidney:	n/a
38	chr17:18215543-18215593	MCF-7	breast:	n/a
39	chr17:18215543-18215593	SKMC	muscle:	n/a
40	chr17:18215543-18215593	NHBE	bronchial:	n/a
41	chr17:18215543-18215593	GM12878	blood:	n/a
42	chr17:18215543-18215593	HPAEpiC	pulmonary alveolar:	n/a
43	chr17:18215543-18215593	T-47D	breast:	n/a
44	chr17:18215543-18215593	GM12892	blood:	n/a
45	chr17:18215543-18215593	MCF10A-Er-Src	breast:	n/a
46	chr17:18215543-18215593	ovcar-3	ovarian:	n/a
47	chr17:18215543-18215593	HepG2	liver:	n/a
48	chr17:18215543-18215593	Jurkat	blood:	n/a
49	chr17:18215543-18215593	BE2_C	brain:	n/a
50	chr17:18215543-18215593	HUVEC	blood vessel:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18204042..18206073-chr17:18215565..18218215,2	MCF-7	breast:
2	chr17:18207672..18211933-chr17:18214098..18218432,6	MCF-7	breast:
3	chr17:18185665..18188160-chr17:18215584..18219242,3	MCF-7	breast:
4	chr17:18156705..18166530-chr17:18215131..18220177,19	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMCR8-2	chr17:18215218-18215965	NONHSAT146173

No data

Variant related genes	Relation type
RPL21P121	TF binding region
SMCR8	TF binding region
SMCR8	CpG island
RPL21P121	CpG island
ENSG00000177427	Chromatin interaction
ENSG00000177731	Chromatin interaction
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11868259	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870126	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936652	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12936769	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12937300	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12939092	0.82[EUR][1000 genomes]
rs12939259	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939357	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939757	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945597	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946058	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949983	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952556	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952667	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563631	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563633	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979276	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979277	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2230154	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273028	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273030	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386456	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2386457	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2386458	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605142	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746023	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746024	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28419113	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764405	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794771	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794772	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829583	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632181	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924750	0.81[EUR][1000 genomes]
rs4924842	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924843	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924845	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924847	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924849	0.83[EUR][1000 genomes]
rs4925160	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925162	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925163	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925167	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925169	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925171	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925172	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58215032	0.90[EUR][1000 genomes]
rs6502643	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502644	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502646	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502649	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66903818	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207123	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215839	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7222684	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7223122	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068602	0.87[EUR][1000 genomes]
rs8068854	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070633	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8071231	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073464	0.83[EUR][1000 genomes]
rs8074444	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080966	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921865	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921866	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921986	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941451	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9898631	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12949078	SHMT1	cis	Esophagus Muscularis	GTEx
rs12949078	SHMT1	cis	Muscle Skeletal	GTEx
rs12949078	SHMT1	cis	Artery Tibial	GTEx
rs12949078	LLGL1	cis	Esophagus Mucosa	GTEx
rs12949078	LGALS9C	cis	Whole Blood	GTEx
rs12949078	SHMT1	cis	multi-tissue	Pritchard
rs12949078	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:18194600-18215600	Weak transcription	Fetal Heart	heart
4	chr17:18196800-18217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:18201800-18216200	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr17:18202200-18216600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr17:18202400-18215600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:18202400-18215600	Strong transcription	Fetal Thymus	thymus
9	chr17:18202400-18216000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:18202400-18216000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:18202400-18216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:18202400-18216200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:18202400-18216400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:18202400-18216400	Strong transcription	Fetal Stomach	stomach
15	chr17:18202400-18216600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr17:18202400-18216600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:18202400-18216600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr17:18202400-18216600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr17:18202600-18215600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr17:18202600-18215600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:18202600-18215800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:18203200-18216800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr17:18206800-18217000	Weak transcription	Stomach Mucosa	stomach
24	chr17:18208800-18217000	Weak transcription	Right Ventricle	heart
25	chr17:18210200-18217000	Weak transcription	Psoas Muscle	Psoas
26	chr17:18210600-18215600	Weak transcription	Fetal Kidney	kidney
27	chr17:18210600-18216400	Weak transcription	Small Intestine	intestine
28	chr17:18210600-18216600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr17:18210600-18217200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:18210800-18215600	Weak transcription	Colon Smooth Muscle	Colon
31	chr17:18211200-18216200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr17:18211200-18216400	Weak transcription	Primary B cells from cord blood	blood
33	chr17:18211200-18216800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:18211200-18217000	Weak transcription	Ovary	ovary
35	chr17:18211200-18217200	Weak transcription	Aorta	Aorta
36	chr17:18211800-18215600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr17:18211800-18215600	Weak transcription	HSMMtube	muscle
38	chr17:18212000-18216200	Weak transcription	HUVEC	blood vessel
39	chr17:18212200-18216400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr17:18212400-18215600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr17:18212400-18215600	Strong transcription	Thymus	Thymus
42	chr17:18212600-18216000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:18212600-18216600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:18213200-18215600	Strong transcription	A549	lung
45	chr17:18213200-18215800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr17:18213400-18215800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr17:18213400-18216000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr17:18213600-18215600	Strong transcription	Fetal Lung	lung
49	chr17:18213600-18216200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr17:18213800-18215600	Strong transcription	NHLF	lung

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