Variant report

Variant	rs2969490
Chromosome Location	chr2:96803904-96803905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr2:96803134-96803957	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:96802981-96804244	Hela-S3	cervix:	n/a	n/a
3	PBX3	chr2:96803521-96804739	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:96803032-96805938	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:96799588-96805762	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:96802923-96814679	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:96803038-96805865	GM12878	blood:	n/a	n/a
8	ELF1	chr2:96803366-96804241	GM12878	blood:	n/a	n/a
9	BCL11A	chr2:96803885-96804154	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:96797189-96814534	GM12892	blood:	n/a	n/a
11	POLR2A	chr2:96803005-96805758	GM18505	blood:	n/a	n/a
12	POLR2A	chr2:96802771-96805555	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:96800040-96811369	IMR90	lung:	n/a	n/a
14	POLR2A	chr2:96803331-96805419	GM15510	blood:	n/a	n/a
15	POLR2A	chr2:96803204-96805708	GM12892	blood:	n/a	n/a
16	PAX5	chr2:96803340-96804215	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:96802751-96813556	GM12892	blood:	n/a	n/a
18	POLR2A	chr2:96803143-96805678	GM12878	blood:	n/a	n/a
19	NFATC1	chr2:96803000-96805569	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:96803618-96805386	GM18526	blood:	n/a	n/a
21	POLR2A	chr2:96803003-96814644	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:96803051-96812890	GM12878	blood:	n/a	n/a
23	MTA3	chr2:96803074-96805367	GM12878	blood:	n/a	n/a
24	PBX3	chr2:96803773-96804633	GM12878	blood:	n/a	n/a
25	POU2F2	chr2:96803311-96804315	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:96797138-96814645	GM12892	blood:	n/a	n/a
27	POLR2A	chr2:96802761-96814437	GM12878	blood:	n/a	n/a
28	POU2F2	chr2:96803194-96805778	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:96797060-96814791	GM12878	blood:	n/a	n/a
30	POU2F2	chr2:96803389-96805424	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:96803054-96805782	GM19099	blood:	n/a	n/a
32	POLR2A	chr2:96802889-96805924	GM19193	blood:	n/a	n/a
33	POLR2A	chr2:96803829-96803956	H1-hESC	embryonic stem cell:	n/a	n/a
34	ATF2	chr2:96803869-96804139	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:96801230-96805978	GM12891	blood:	n/a	n/a
36	ZEB1	chr2:96803834-96805193	GM12878	blood:	n/a	chr2:96804540-96804549
37	POU2F2	chr2:96803158-96803915	GM12891	blood:	n/a	n/a
38	PML	chr2:96803695-96805526	GM12878	blood:	n/a	n/a
39	NFATC1	chr2:96803094-96804308	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:96802764-96805936	GM12892	blood:	n/a	n/a
41	POLR2A	chr2:96803072-96804316	GM12891	blood:	n/a	n/a
42	POLR2A	chr2:96803037-96805451	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96802498..96805773-chr2:96872667..96874693,3	MCF-7	breast:
2	chr2:96802971..96805127-chr2:96925819..96928248,3	MCF-7	breast:

No data

Variant related genes	Relation type
ASTL	TF binding region
ENSG00000135956	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10183151	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs1030864	0.84[EUR][1000 genomes]
rs11680950	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs1168965	0.81[CEU][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs1168966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168967	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168968	0.86[CEU][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs1168970	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1168972	0.84[EUR][1000 genomes]
rs1168974	0.86[CEU][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs1168975	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1168976	0.86[CEU][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs13009727	0.83[EUR][1000 genomes]
rs13019188	0.94[CEU][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs1657502	0.95[CEU][hapmap];0.84[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1724121	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1724125	0.82[EUR][1000 genomes]
rs2229169	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs2252697	0.93[EUR][1000 genomes]
rs2301707	0.86[CEU][hapmap]
rs2312955	0.86[GIH][hapmap];0.80[EUR][1000 genomes]
rs2576437	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2579519	0.89[GIH][hapmap]
rs2692894	0.81[CEU][hapmap];0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs2917662	0.81[EUR][1000 genomes]
rs2918916	0.85[EUR][1000 genomes]
rs2969491	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs3111873	0.81[EUR][1000 genomes]
rs3821051	0.86[CEU][hapmap]
rs4426564	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs4907299	0.81[EUR][1000 genomes]
rs749457	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs749459	0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7561198	0.80[EUR][1000 genomes]
rs7604842	0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs772175	0.86[CEU][hapmap]
rs772178	0.86[CEU][hapmap]
rs893173	0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	esv3419661	chr2:96803250-96805798	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2969490	FAHD2CP	cis	lung	GTEx
rs2969490	ADRA2B	cis	Thyroid	GTEx
rs2969490	KIAA1310	cis	cerebellum	SCAN
rs2969490	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs2969490	MRPL30	cis	parietal	SCAN
rs2969490	FAHD2CP	cis	Muscle Skeletal	GTEx
rs2969490	GPAT2	cis	Muscle Skeletal	GTEx
rs2969490	FAHD2CP	cis	Artery Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96786400-96804200	Weak transcription	Primary B cells from cord blood	blood
2	chr2:96787800-96807800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr2:96788200-96804400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:96789800-96804400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr2:96792000-96808000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:96795800-96804000	Weak transcription	Fetal Thymus	thymus
7	chr2:96796000-96804800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:96798000-96809400	Weak transcription	Gastric	stomach
9	chr2:96800000-96804800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:96802000-96805400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr2:96802000-96805400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:96802200-96804400	Weak transcription	Thymus	Thymus
13	chr2:96802600-96810200	Weak transcription	HSMMtube	muscle
14	chr2:96803000-96804600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:96803000-96805400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:96803200-96805200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:96803400-96804000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr2:96803400-96805000	Weak transcription	Primary T cells from cord blood	blood
19	chr2:96803400-96805400	Enhancers	Esophagus	oesophagus
20	chr2:96803400-96805400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr2:96803600-96804000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:96803600-96804200	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr2:96803600-96804400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr2:96803600-96805200	Enhancers	Colonic Mucosa	Colon
25	chr2:96803600-96805600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:96803600-96808000	Weak transcription	Spleen	Spleen
27	chr2:96803600-96809200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:96803800-96804000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:96803800-96804200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr2:96803800-96804400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:96803800-96804800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:96803800-96805400	Enhancers	HUES48 Cell Line	embryonic stem cell

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