Variant report

Variant	rs17281287
Chromosome Location	chr3:150421419-150421420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:178)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:178 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:150421390-150421435	GM19238	blood:	n/a	n/a
2	CTCF	chr3:150421359-150421558	MCF-7	breast:	n/a	n/a
3	CTCF	chr3:150421340-150421490	HRE	kidney:	n/a	n/a
4	CBX3	chr3:150420960-150422063	K562	blood:	n/a	n/a
5	ZNF143	chr3:150421379-150421918	GM12878	blood:	n/a	n/a
6	CTCF	chr3:150421346-150421624	GM19239	blood:	n/a	n/a
7	CTBP2	chr3:150421076-150421961	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:150421153-150422204	GM18505	blood:	n/a	n/a
9	MAX	chr3:150420869-150422243	A549	lung:	n/a	n/a
10	CHD2	chr3:150421323-150422170	Hela-S3	cervix:	n/a	chr3:150421690-150421700
11	POLR2A	chr3:150420786-150422063	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr3:150421266-150421899	A549	lung:	n/a	n/a
13	YY1	chr3:150421406-150421791	A549	lung:	n/a	n/a
14	ZBTB33	chr3:150421105-150422148	SK-N-SH	brain:	n/a	chr3:150421737-150421752 chr3:150421737-150421747
15	HCFC1	chr3:150421406-150422368	Hela-S3	cervix:	n/a	n/a
16	MYC	chr3:150421404-150421576	MCF-7	breast:	n/a	n/a
17	MAX	chr3:150421020-150422101	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:150421297-150422048	SK-N-MC	brain:	n/a	n/a
19	YY1	chr3:150421325-150422070	H1-hESC	embryonic stem cell:	n/a	n/a
20	HA-E2F1	chr3:150421334-150422263	MCF-7	breast:	n/a	chr3:150421964-150421981 chr3:150421967-150421978
21	ELF1	chr3:150421238-150422237	MCF-7	breast:	n/a	n/a
22	RCOR1	chr3:150421285-150422039	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:150421103-150422017	ProgFib	skin:	n/a	n/a
24	EGR1	chr3:150421136-150421684	GM12878	blood:	n/a	chr3:150421267-150421280
25	POLR2A	chr3:150421115-150422054	GM12892	blood:	n/a	n/a
26	RELA	chr3:150421354-150422145	GM15510	blood:	n/a	n/a
27	POLR2A	chr3:150421109-150422131	MCF-7	breast:	n/a	n/a
28	CTCF	chr3:150421300-150421450	AG09319	gingival:	n/a	n/a
29	POLR2A	chr3:150421325-150421829	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr3:150421257-150422172	HL-60	blood:	n/a	n/a
31	NFIC	chr3:150421405-150422030	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr3:150421182-150422026	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:150421167-150421911	A549	lung:	n/a	n/a
34	MTA3	chr3:150420831-150422205	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:150420948-150422142	GM12892	blood:	n/a	n/a
36	MAX	chr3:150421043-150422124	A549	lung:	n/a	n/a
37	TAF1	chr3:150421377-150422019	A549	lung:	n/a	n/a
38	POLR2A	chr3:150421271-150422006	GM12892	blood:	n/a	n/a
39	CHD1	chr3:150421283-150421553	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:150421154-150422203	U87	brain:	n/a	n/a
41	POLR2A	chr3:150421292-150421994	GM12891	blood:	n/a	n/a
42	POLR2A	chr3:150421324-150421963	HUVEC	blood vessel:	n/a	n/a
43	ZBTB33	chr3:150421224-150422114	SK-N-SH	brain:	n/a	chr3:150421737-150421752 chr3:150421737-150421747
44	REST	chr3:150421366-150422302	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr3:150421286-150421923	GM10847	blood:	n/a	n/a
46	REST	chr3:150421404-150421934	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr3:150421226-150421956	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:150421305-150422159	GM12878	blood:	n/a	n/a
49	NFIC	chr3:150421253-150422228	GM12878	blood:	n/a	n/a
50	RUNX3	chr3:150421168-150422184	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150320651..150322535-chr3:150420731..150422273,2	K562	blood:
2	chr3:150320068..150322587-chr3:150419780..150423653,7	MCF-7	breast:
3	chr3:150319300..150322608-chr3:150420316..150423261,6	MCF-7	breast:
4	chr3:150419019..150423394-chr3:150479448..150481415,4	MCF-7	breast:
5	chr3:150421205..150424923-chr3:150480120..150484463,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-392O18.1.1-1	chr3:150421351-150421454	ENSG00000240137.1

No data

Variant related genes	Relation type
ENSG00000240137	TF binding region
ENSG00000181788	Chromatin interaction
ENSG00000244265	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000198843	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1131685	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719012	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12494272	0.83[ASN][1000 genomes]
rs12630292	0.83[ASN][1000 genomes]
rs13063408	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065451	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13068979	0.97[EUR][1000 genomes]
rs13074103	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13074670	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079739	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13079755	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13085974	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13086215	0.97[EUR][1000 genomes]
rs13086267	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13086869	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13090897	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16862794	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1897489	0.83[ASN][1000 genomes]
rs1897491	0.83[ASN][1000 genomes]
rs1897494	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2869477	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs28790675	0.82[ASN][1000 genomes]
rs4558804	0.83[ASN][1000 genomes]
rs4571271	0.96[EUR][1000 genomes]
rs476663	0.84[JPT][hapmap]
rs5007703	0.97[EUR][1000 genomes]
rs57680627	0.98[ASN][1000 genomes]
rs59885616	0.93[ASN][1000 genomes]
rs6766333	0.83[ASN][1000 genomes]
rs6807493	0.86[ASN][1000 genomes]
rs73869266	0.81[ASN][1000 genomes]
rs73869279	0.86[ASN][1000 genomes]
rs7648424	0.83[ASN][1000 genomes]
rs7650706	0.83[ASN][1000 genomes]
rs9682958	0.81[ASN][1000 genomes]
rs9848451	0.83[ASN][1000 genomes]
rs9876621	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17281287	FAM194A	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150420800-150421600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:150420800-150421600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:150420800-150421600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr3:150420800-150422200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:150420800-150422200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:150420800-150422200	Active TSS	Brain Angular Gyrus	brain
7	chr3:150420800-150422200	Active TSS	Brain Hippocampus Middle	brain
8	chr3:150420800-150422200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr3:150420800-150422200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:150420800-150422200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:150420800-150422200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr3:150420800-150422200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:150420800-150422200	Active TSS	Rectal Smooth Muscle	rectum
14	chr3:150420800-150422200	Active TSS	Thymus	Thymus
15	chr3:150420800-150422400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:150420800-150422400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:150420800-150422400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:150420800-150422400	Active TSS	Colon Smooth Muscle	Colon
19	chr3:150420800-150422400	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr3:150420800-150422600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:150420800-150422600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:150420800-150422600	Active TSS	A549	lung
23	chr3:150421000-150421600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:150421000-150421600	Flanking Active TSS	Pancreas	Pancrea
25	chr3:150421000-150421600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr3:150421000-150421600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr3:150421000-150421800	Active TSS	Primary hematopoietic stem cells	blood
28	chr3:150421000-150422000	Active TSS	Gastric	stomach
29	chr3:150421000-150422000	Active TSS	HSMMtube	muscle
30	chr3:150421000-150422000	Active TSS	Osteobl	bone
31	chr3:150421000-150422200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:150421000-150422200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:150421000-150422200	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr3:150421000-150422200	Active TSS	Brain Anterior Caudate	brain
35	chr3:150421000-150422200	Active TSS	Brain Cingulate Gyrus	brain
36	chr3:150421000-150422200	Active TSS	Brain Substantia Nigra	brain
37	chr3:150421000-150422200	Active TSS	Esophagus	oesophagus
38	chr3:150421000-150422200	Active TSS	Fetal Intestine Large	intestine
39	chr3:150421000-150422200	Active TSS	Fetal Kidney	kidney
40	chr3:150421000-150422200	Active TSS	Fetal Lung	lung
41	chr3:150421000-150422200	Active TSS	Ovary	ovary
42	chr3:150421000-150422400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:150421000-150422400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:150421000-150422400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:150421000-150422400	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr3:150421000-150422400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:150421000-150422400	Active TSS	Psoas Muscle	Psoas
48	chr3:150421000-150422400	Active TSS	Right Atrium	heart
49	chr3:150421000-150422400	Active TSS	Right Ventricle	heart
50	chr3:150421000-150422400	Active TSS	Sigmoid Colon	Sigmoid Colon

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