Variant report

Variant	rs3111873
Chromosome Location	chr2:96781986-96781987
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr2:96781670-96781993	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr2:96781386-96782483	H1-hESC	embryonic stem cell:	n/a	n/a
3	HA-E2F1	chr2:96781930-96783103	MCF-7	breast:	n/a	chr2:96782795-96782804 chr2:96782210-96782219 chr2:96782292-96782302 chr2:96782654-96782664 chr2:96782914-96782924 chr2:96782437-96782449 chr2:96782243-96782252
4	GABPA	chr2:96781487-96782436	H1-hESC	embryonic stem cell:	n/a	chr2:96782216-96782225 chr2:96782210-96782219
5	CTBP2	chr2:96781457-96783861	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZBTB7A	chr2:96781936-96783021	ECC-1	luminal epithelium:	n/a	chr2:96782209-96782218 chr2:96782904-96782913
7	POLR2A	chr2:96781780-96782606	H1-hESC	embryonic stem cell:	n/a	n/a
8	TBP	chr2:96781973-96782449	H1-hESC	embryonic stem cell:	n/a	n/a
9	BACH1	chr2:96781886-96783188	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZNF263	chr2:96781869-96783220	HEK293-T-REx	kidney:	n/a	n/a
11	ELF1	chr2:96781946-96783152	GM12878	blood:	n/a	chr2:96782648-96782660 chr2:96782087-96782099 chr2:96782922-96782934 chr2:96782758-96782770 chr2:96782515-96782527
12	E2F6	chr2:96781705-96782576	H1-hESC	embryonic stem cell:	n/a	chr2:96782210-96782219 chr2:96782292-96782302 chr2:96782437-96782449 chr2:96782243-96782252 chr2:96781891-96781903
13	E2F6	chr2:96781508-96782519	H1-hESC	embryonic stem cell:	n/a	chr2:96782210-96782219 chr2:96782292-96782302 chr2:96782437-96782449 chr2:96782243-96782252 chr2:96781891-96781903
14	MAX	chr2:96781425-96782518	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3A	chr2:96781628-96783146	H1-hESC	embryonic stem cell:	n/a	chr2:96781982-96781995 chr2:96782213-96782226 chr2:96782836-96782849 chr2:96782833-96782842 chr2:96782553-96782566 chr2:96782177-96782188 chr2:96782453-96782466
16	MAX	chr2:96781619-96782317	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr2:96781607-96782159	H1-hESC	embryonic stem cell:	n/a	chr2:96781987-96781996 chr2:96781987-96782001

No.	Distal block	Cell Line	Cell type
1	chr2:96781378..96786213-chr2:96808688..96812498,6	MCF-7	breast:
2	chr2:96656483..96658831-chr2:96781728..96784486,2	K562	blood:
3	chr2:96781942..96784647-chr2:96809826..96814461,4	MCF-7	breast:
4	chr2:96781026..96783523-chr2:96872750..96874386,2	MCF-7	breast:

Variant related genes	Relation type
ADRA2B	TF binding region
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000158050	Chromatin interaction
ENSG00000228873	Chromatin interaction
ENSG00000174501	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10183151	0.97[EUR][1000 genomes]
rs1030864	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168965	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168966	0.80[EUR][1000 genomes]
rs1168968	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168970	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168972	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168974	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168975	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168976	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13019188	0.83[EUR][1000 genomes]
rs1657502	0.82[EUR][1000 genomes]
rs1724125	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2140938	0.90[EUR][1000 genomes]
rs2229169	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252697	0.82[EUR][1000 genomes]
rs2312955	0.88[AFR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576437	0.81[EUR][1000 genomes]
rs2579549	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2579550	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2579552	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2692893	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2692894	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2692934	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2692935	0.85[EUR][1000 genomes]
rs2692936	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2692937	0.92[EUR][1000 genomes]
rs2917662	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2969490	0.81[EUR][1000 genomes]
rs2969491	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907299	0.96[EUR][1000 genomes]
rs749457	0.81[EUR][1000 genomes]
rs7561198	0.88[AFR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604842	0.97[EUR][1000 genomes]
rs893173	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
7	nsv1000049	chr2:96740430-96796312	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
9	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription 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	156 gene(s)	inside rSNPs	diseases
10	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv874676	chr2:96753149-96825363	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv1008495	chr2:96755070-96825363	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv1002392	chr2:96756289-96815149	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
16	nsv1004977	chr2:96757107-96819188	Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv1015000	chr2:96757107-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	162 gene(s)	inside rSNPs	diseases
19	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh 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	162 gene(s)	inside rSNPs	diseases
20	nsv1007132	chr2:96767204-96829489	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv2834	chr2:96772925-96785110	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
22	nsv874678	chr2:96777340-96786411	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3111873	GPAT2	cis	Adipose Subcutaneous	GTEx
rs3111873	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs3111873	FAHD2CP	cis	Muscle Skeletal	GTEx
rs3111873	ADRA2B	cis	Nerve Tibial	GTEx
rs3111873	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs3111873	GPAT2	cis	Muscle Skeletal	GTEx
rs3111873	ADRA2B	cis	Thyroid	GTEx
rs3111873	FAHD2CP	cis	lung	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96772000-96782200	Weak transcription	Liver	Liver
2	chr2:96780400-96783000	Active TSS	Left Ventricle	heart
3	chr2:96780600-96782000	Bivalent Enhancer	Placenta	Placenta
4	chr2:96781000-96782000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:96781000-96783000	Active TSS	Rectal Smooth Muscle	rectum
6	chr2:96781400-96782000	Bivalent Enhancer	Ovary	ovary
7	chr2:96781400-96782200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:96781400-96782400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
9	chr2:96781400-96783000	Active TSS	Esophagus	oesophagus
10	chr2:96781600-96782000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr2:96781600-96782000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
12	chr2:96781600-96782000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr2:96781600-96782000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr2:96781600-96782000	Bivalent Enhancer	Fetal Stomach	stomach
15	chr2:96781600-96782200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:96781600-96782200	Bivalent Enhancer	Brain Substantia Nigra	brain
17	chr2:96781600-96782200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
18	chr2:96781600-96782200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
19	chr2:96781600-96782800	Flanking Active TSS	Right Ventricle	heart
20	chr2:96781600-96783000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr2:96781600-96783000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr2:96781600-96783000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr2:96781600-96783000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:96781600-96783000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:96781600-96783400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:96781800-96782000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:96781800-96782000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:96781800-96782000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:96781800-96782000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
30	chr2:96781800-96782000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
31	chr2:96781800-96782000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:96781800-96782000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr2:96781800-96782000	Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr2:96781800-96782000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:96781800-96782000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:96781800-96782000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:96781800-96782000	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
38	chr2:96781800-96782000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:96781800-96782000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
40	chr2:96781800-96782000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
41	chr2:96781800-96782200	Enhancers	Primary B cells from cord blood	blood
42	chr2:96781800-96782200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr2:96781800-96782200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:96781800-96782200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:96781800-96782200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:96781800-96782200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:96781800-96782200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
48	chr2:96781800-96782200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr2:96781800-96782200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
50	chr2:96781800-96782200	Bivalent Enhancer	Lung	lung

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