Variant report

Variant	rs2244996
Chromosome Location	chr3:158519446-158519447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:179)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:179 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr3:158519390-158520060	A549	lung:	n/a	n/a
2	POLR2A	chr3:158519012-158520264	HUVEC	blood vessel:	n/a	n/a
3	GATA3	chr3:158519102-158520263	A549	lung:	n/a	n/a
4	RCOR1	chr3:158519379-158520799	K562	blood:	n/a	n/a
5	POLR2A	chr3:158519357-158520436	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:158519411-158520339	GM15510	blood:	n/a	n/a
7	SIN3AK20	chr3:158519314-158520361	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:158519432-158520348	K562	blood:	n/a	n/a
9	MAX	chr3:158518993-158520599	HepG2	liver:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
10	POLR2A	chr3:158519430-158520129	PFSK-1	brain:	n/a	n/a
11	TAF1	chr3:158519381-158520163	ECC-1	luminal epithelium:	n/a	n/a
12	HCFC1	chr3:158519363-158520446	K562	blood:	n/a	n/a
13	POLR2A	chr3:158519048-158520423	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:158519310-158521018	HL-60	blood:	n/a	n/a
15	POLR2A	chr3:158519428-158520341	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:158518843-158520542	IMR90	lung:	n/a	n/a
17	NR2F2	chr3:158519337-158520658	K562	blood:	n/a	n/a
18	ATF3	chr3:158519433-158520028	K562	blood:	n/a	n/a
19	USF1	chr3:158519291-158520378	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:158519257-158520430	MCF10A-Er-Src	breast:	n/a	n/a
21	RFX5	chr3:158519428-158519916	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:158519402-158520254	H1-neurons	neurons:	n/a	n/a
23	USF1	chr3:158519414-158520112	GM12878	blood:	n/a	n/a
24	E2F6	chr3:158519355-158520366	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr3:158519428-158520581	NB4	blood:	n/a	n/a
26	TCF7L2	chr3:158519435-158520099	HCT-116	colon:	n/a	n/a
27	POLR2A	chr3:158519239-158520249	HepG2	liver:	n/a	n/a
28	ATF3	chr3:158519327-158520052	A549	lung:	n/a	n/a
29	EP300	chr3:158519403-158519984	GM12878	blood:	n/a	n/a
30	MAX	chr3:158519318-158520391	SK-N-SH	brain:	n/a	chr3:158520189-158520198
31	ZNF263	chr3:158519437-158520199	HEK293-T-REx	kidney:	n/a	n/a
32	NFIC	chr3:158519276-158520095	GM12878	blood:	n/a	n/a
33	E2F6	chr3:158519244-158520429	A549	lung:	n/a	n/a
34	RUNX3	chr3:158519188-158520048	GM12878	blood:	n/a	n/a
35	JUND	chr3:158519444-158520060	A549	lung:	n/a	n/a
36	USF1	chr3:158519436-158520650	K562	blood:	n/a	n/a
37	TCF12	chr3:158519327-158520337	ECC-1	luminal epithelium:	n/a	n/a
38	MAX	chr3:158519442-158520213	HCT-116	colon:	n/a	chr3:158520189-158520198
39	MAX	chr3:158519176-158520231	A549	lung:	n/a	chr3:158520189-158520198
40	CREB1	chr3:158519366-158520206	HepG2	liver:	n/a	n/a
41	FOXM1	chr3:158519432-158520073	GM12878	blood:	n/a	n/a
42	USF1	chr3:158519367-158520172	A549	lung:	n/a	n/a
43	MYC	chr3:158519286-158520734	K562	blood:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
44	MYC	chr3:158519352-158520748	K562	blood:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
45	MAX	chr3:158519425-158520721	GM12878	blood:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
46	HA-E2F1	chr3:158518788-158520590	MCF-7	breast:	n/a	n/a
47	HEY1	chr3:158519338-158520098	HepG2	liver:	n/a	n/a
48	MAX	chr3:158519262-158520556	A549	lung:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
49	SMARCB1	chr3:158519420-158520659	Hela-S3	cervix:	n/a	n/a
50	SIN3A	chr3:158519005-158520527	H1-hESC	embryonic stem cell:	n/a	chr3:158519699-158519713

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:158519410-158519460	GM12892	blood:	n/a
2	chr3:158519410-158519460	GM12891	blood:	n/a
3	chr3:158519410-158519460	SKMC	muscle:	n/a
4	chr3:158519410-158519460	BE2_C	brain:	n/a
5	chr3:158519410-158519460	ECC-1	luminal epithelium:	n/a
6	chr3:158519410-158519460	MCF-7	breast:	n/a
7	chr3:158519410-158519460	SK-N-MC	brain:	n/a
8	chr3:158519410-158519460	GM06990	blood:	n/a
9	chr3:158519410-158519460	PrEC	prostate:	n/a
10	chr3:158519410-158519460	NHDF-neo	bronchial:	n/a
11	chr3:158519410-158519460	NB4	blood:	n/a
12	chr3:158519410-158519460	NT2-D1	testis:	n/a
13	chr3:158519410-158519460	HIPEpiC	eye:	n/a
14	chr3:158519410-158519460	HCM	heart:	n/a
15	chr3:158519410-158519460	HCPEpiC	choroid plexus:	n/a
16	chr3:158519410-158519460	HEEpiC	esophagus:	n/a
17	chr3:158519410-158519460	MCF10A-Er-Src	breast:	n/a
18	chr3:158519410-158519460	AG09319	gingival:	n/a
19	chr3:158519410-158519460	HCF	heart:	n/a
20	chr3:158519410-158519460	PFSK-1	brain:	n/a
21	chr3:158519410-158519460	HUVEC	blood vessel:	n/a
22	chr3:158519410-158519460	HRE	kidney:	n/a
23	chr3:158519410-158519460	Caco-2	colon:	n/a
24	chr3:158519410-158519460	K562	blood:	n/a
25	chr3:158519410-158519460	HRCEpiC	kidney:	n/a
26	chr3:158519410-158519460	NHBE	bronchial:	n/a
27	chr3:158519410-158519460	AG04449	skin:	fetal
28	chr3:158519410-158519460	H1-hESC	embryonic stem cell:	embryo
29	chr3:158519410-158519460	SAEC	small airway:	n/a
30	chr3:158519410-158519460	AG09309	skin:	n/a
31	chr3:158519410-158519460	BJ	skin:	n/a
32	chr3:158519410-158519460	HMEC	breast:	n/a
33	chr3:158519410-158519460	SK-N-SH_RA	brain:	n/a
34	chr3:158519410-158519460	U87	brain:	n/a
35	chr3:158519410-158519460	RPTEC	kidney:	n/a
36	chr3:158519410-158519460	HPAEpiC	pulmonary alveolar:	n/a
37	chr3:158519410-158519460	AoSMC	blood vessel:	n/a
38	chr3:158519410-158519460	Hela-S3	cervix:	n/a
39	chr3:158519410-158519460	CMK	blood:	n/a
40	chr3:158519410-158519460	HL-60	blood:	n/a
41	chr3:158519410-158519460	GM19239	blood:	n/a
42	chr3:158519410-158519460	PANC-1	pancreas:	n/a
43	chr3:158519410-158519460	NH-A	brain:	n/a
44	chr3:158519410-158519460	A549	lung:	n/a
45	chr3:158519410-158519460	HNPCEpiC	eye:	n/a
46	chr3:158519410-158519460	LNCaP	prostate:	n/a
47	chr3:158519410-158519460	AG04450	lung:	fetal
48	chr3:158519410-158519460	IMR90	lung:	fetal
49	chr3:158519410-158519460	HAEpiC	amniotic membrane:	n/a
50	chr3:158519410-158519460	ProgFib	skin:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:158360988..158362549-chr3:158517154..158519715,2	K562	blood:
2	chr3:158519080..158523533-chr3:158523571..158529220,8	MCF-7	breast:
3	chr15:75660196..75660788-chr3:158519289..158520156,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RARRES1-3	chr3:158519046-158519724	ENSG00000272247.1

No data

Variant related genes	Relation type
MFSD1	TF binding region
MFSD1	CpG island
ENSG00000118855	Chromatin interaction
ENSG00000168827	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10936160	0.88[ASN][1000 genomes]
rs12493280	0.88[ASN][1000 genomes]
rs12638831	0.88[ASN][1000 genomes]
rs1381463	0.88[ASN][1000 genomes]
rs2364921	0.95[ASN][1000 genomes]
rs2615052	0.82[EUR][1000 genomes]
rs2713736	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802844	0.97[ASN][1000 genomes]
rs7429205	0.89[ASN][1000 genomes]
rs9861042	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2244996	RP11-379F4.9	cis	Thyroid	GTEx
rs2244996	RP11-379F4.9	cis	Muscle Skeletal	GTEx
rs2244996	RP11-379F4.9	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158518600-158519600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:158518600-158519600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:158518600-158519600	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:158518600-158520200	Active TSS	Brain Anterior Caudate	brain
5	chr3:158518600-158520600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:158518600-158521400	Active TSS	Brain Cingulate Gyrus	brain
7	chr3:158518800-158519600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:158518800-158519600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr3:158518800-158519600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr3:158518800-158519600	Flanking Active TSS	Liver	Liver
11	chr3:158518800-158519600	Flanking Active TSS	Fetal Lung	lung
12	chr3:158518800-158519600	Flanking Active TSS	HUVEC	blood vessel
13	chr3:158518800-158519600	Flanking Active TSS	NH-A	brain
14	chr3:158518800-158519600	Flanking Active TSS	NHDF-Ad	bronchial
15	chr3:158518800-158519800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:158518800-158519800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr3:158518800-158519800	Flanking Active TSS	Fetal Brain Male	brain
18	chr3:158518800-158519800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr3:158518800-158519800	Flanking Active TSS	HSMM	muscle
20	chr3:158518800-158520400	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:158518800-158520600	Active TSS	Fetal Heart	heart
22	chr3:158518800-158520600	Active TSS	Left Ventricle	heart
23	chr3:158518800-158520600	Active TSS	Pancreas	Pancrea
24	chr3:158518800-158520800	Active TSS	Colonic Mucosa	Colon
25	chr3:158518800-158520800	Active TSS	Fetal Intestine Large	intestine
26	chr3:158518800-158520800	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:158518800-158521200	Active TSS	Psoas Muscle	Psoas
28	chr3:158518800-158521400	Active TSS	Brain Hippocampus Middle	brain
29	chr3:158518800-158522000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:158519000-158519600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:158519000-158519600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr3:158519000-158519600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr3:158519000-158519600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr3:158519000-158519600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr3:158519000-158519600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:158519000-158519600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
37	chr3:158519000-158519600	Active TSS	HepG2	liver
38	chr3:158519000-158519600	Flanking Active TSS	HSMMtube	muscle
39	chr3:158519000-158519600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr3:158519000-158519800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:158519000-158519800	Flanking Active TSS	HMEC	breast
42	chr3:158519000-158520000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:158519000-158520200	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:158519000-158520400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr3:158519000-158520400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:158519000-158520400	Active TSS	Lung	lung
47	chr3:158519000-158520400	Active TSS	Thymus	Thymus
48	chr3:158519000-158520600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:158519000-158520600	Active TSS	Esophagus	oesophagus
50	chr3:158519000-158520800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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