Variant report

Variant	rs2298952
Chromosome Location	chr3:50286953-50286954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50286483-50287181	HUVEC	blood vessel:	n/a	n/a
2	CEBPB	chr3:50286928-50287252	A549	lung:	n/a	chr3:50287069-50287080
3	CEBPB	chr3:50286887-50287260	Hela-S3	cervix:	n/a	chr3:50287069-50287080
4	CEBPB	chr3:50286936-50287244	HepG2	liver:	n/a	chr3:50287069-50287080
5	CEBPB	chr3:50286884-50287263	IMR90	lung:	n/a	chr3:50287069-50287080
6	TFAP2C	chr3:50286742-50287178	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50285794..50287814-chr3:50306650..50309079,2	MCF-7	breast:
2	chr3:50286473..50289840-chr3:50357894..50361890,3	MCF-7	breast:
3	chr3:50284602..50287815-chr3:50290818..50293169,4	K562	blood:
4	chr3:50283737..50287668-chr3:50290117..50294367,4	K562	blood:
5	chr3:50283028..50285015-chr3:50286651..50289261,2	MCF-7	breast:
6	chr3:50279236..50281282-chr3:50285946..50288178,2	MCF-7	breast:
7	chr3:50275603..50278218-chr3:50286370..50288420,2	MCF-7	breast:
8	chr3:50263658..50265512-chr3:50286295..50288716,2	K562	blood:
9	chr3:50285711..50287237-chr3:50303937..50306020,2	MCF-7	breast:
10	chr3:50272949..50274999-chr3:50285398..50287724,2	MCF-7	breast:

No data

Variant related genes	Relation type
GNAI2	TF binding region
ENSG00000114353	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000068001	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000213600	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11716820	0.88[AMR][1000 genomes]
rs1540293	0.91[CEU][hapmap]
rs2236974	0.91[CEU][hapmap]
rs56122560	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9832454	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
7	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
11	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
12	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
19	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
20	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
21	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
23	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
24	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
25	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
26	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
27	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
28	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50276200-50287000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:50276400-50294400	Genic enhancers	Lung	lung
3	chr3:50278600-50287400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:50283400-50293200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:50283800-50287200	Enhancers	Gastric	stomach
6	chr3:50283800-50289000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:50283800-50289400	Enhancers	Left Ventricle	heart
8	chr3:50283800-50294000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:50284000-50289000	Enhancers	Brain Cingulate Gyrus	brain
10	chr3:50284000-50289200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:50284000-50289400	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr3:50284200-50287000	Genic enhancers	Fetal Intestine Large	intestine
13	chr3:50284200-50287400	Genic enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:50284200-50287400	Weak transcription	Pancreas	Pancrea
15	chr3:50284200-50287800	Enhancers	HMEC	breast
16	chr3:50284200-50287800	Genic enhancers	NHLF	lung
17	chr3:50284200-50288200	Enhancers	Right Ventricle	heart
18	chr3:50284200-50288600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr3:50284200-50289600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
20	chr3:50284200-50289600	Enhancers	Right Atrium	heart
21	chr3:50284200-50289800	Enhancers	Stomach Mucosa	stomach
22	chr3:50284200-50297000	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr3:50284400-50287200	Enhancers	Colonic Mucosa	Colon
24	chr3:50284400-50287800	Genic enhancers	Stomach Smooth Muscle	stomach
25	chr3:50284400-50288200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:50284400-50289400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:50284400-50289400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:50284400-50290800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:50284400-50292000	Weak transcription	Fetal Brain Male	brain
30	chr3:50284400-50293000	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr3:50284400-50295000	Genic enhancers	Spleen	Spleen
32	chr3:50284400-50295800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:50284400-50297000	Genic enhancers	Fetal Muscle Leg	muscle
34	chr3:50284600-50287400	Genic enhancers	Primary B cells from cord blood	blood
35	chr3:50284600-50287400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:50284600-50287600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:50284600-50287600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:50284600-50287800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:50284600-50288200	Genic enhancers	Fetal Thymus	thymus
40	chr3:50284600-50288600	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:50284600-50289400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr3:50284600-50294000	Genic enhancers	Placenta	Placenta
43	chr3:50284800-50287000	Enhancers	NH-A	brain
44	chr3:50284800-50287400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:50284800-50287400	Weak transcription	Fetal Brain Female	brain
46	chr3:50284800-50288400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:50284800-50288400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:50284800-50288800	Enhancers	Liver	Liver
49	chr3:50284800-50289800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:50284800-50291000	Weak transcription	HepG2	liver

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