Variant report

Variant	rs2301707
Chromosome Location	chr2:96931846-96931847
allele	A/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	TEAD4	chr2:96931600-96931918	H1-hESC	embryonic stem cell:	n/a	n/a
2	ELK4	chr2:96931473-96932187	HEK293	kidney:	n/a	chr2:96931729-96931738
3	CCNT2	chr2:96931475-96932359	K562	blood:	n/a	n/a
4	SP1	chr2:96931373-96932255	A549	lung:	n/a	chr2:96931771-96931780 chr2:96931769-96931781 chr2:96931416-96931425 chr2:96931770-96931784 chr2:96931770-96931779 chr2:96931753-96931767 chr2:96931412-96931426 chr2:96931415-96931427 chr2:96931415-96931427 chr2:96931770-96931779
5	SPI1	chr2:96931548-96932092	GM12891	blood:	n/a	chr2:96931748-96931761
6	ATF3	chr2:96931589-96932050	K562	blood:	n/a	chr2:96931771-96931780
7	ZEB1	chr2:96931676-96932020	GM12878	blood:	n/a	n/a
8	SIX5	chr2:96931561-96932072	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF384	chr2:96931653-96932170	GM12878	blood:	n/a	n/a
10	SP1	chr2:96931459-96932326	A549	lung:	n/a	chr2:96931771-96931780 chr2:96931769-96931781 chr2:96931770-96931784 chr2:96931770-96931779 chr2:96931753-96931767 chr2:96931770-96931779
11	MXI1	chr2:96930187-96933335	IMR90	lung:	n/a	n/a
12	POLR2A	chr2:96931129-96932589	H1-neurons	neurons:	n/a	n/a
13	TEAD4	chr2:96931529-96932286	ECC-1	luminal epithelium:	n/a	n/a
14	FOXP2	chr2:96931568-96932169	SK-N-MC	brain:	n/a	n/a
15	MAX	chr2:96931557-96932417	K562	blood:	n/a	n/a
16	NFIC	chr2:96931455-96932572	HepG2	liver:	n/a	n/a
17	HCFC1	chr2:96931449-96932486	K562	blood:	n/a	n/a
18	IRF1	chr2:96931478-96932434	K562	blood:	n/a	n/a
19	CTBP2	chr2:96931479-96932363	H1-hESC	embryonic stem cell:	n/a	n/a
20	NRF1	chr2:96931500-96932475	GM12878	blood:	n/a	chr2:96931783-96931792
21	ZBTB33	chr2:96931656-96932034	HCT-116	colon:	n/a	chr2:96931854-96931869
22	POU2F2	chr2:96931526-96932171	GM12891	blood:	n/a	chr2:96931776-96931788
23	YY1	chr2:96931744-96932115	K562	blood:	n/a	chr2:96931803-96931817 chr2:96931800-96931814
24	POLR2A	chr2:96931314-96932516	GM12892	blood:	n/a	n/a
25	TAF1	chr2:96931576-96932409	K562	blood:	n/a	n/a
26	BRCA1	chr2:96931646-96932166	GM12878	blood:	n/a	n/a
27	CREB1	chr2:96931381-96932375	A549	lung:	n/a	n/a
28	MYC	chr2:96931751-96932298	K562	blood:	n/a	n/a
29	JUND	chr2:96931357-96932595	H1-hESC	embryonic stem cell:	n/a	chr2:96931454-96931468
30	POLR2A	chr2:96931833-96932123	H1-hESC	embryonic stem cell:	n/a	n/a
31	SREBP2	chr2:96931342-96932518	GM12878	blood:	n/a	n/a
32	YY1	chr2:96931671-96932333	A549	lung:	n/a	chr2:96931803-96931817 chr2:96931800-96931814
33	HEY1	chr2:96931457-96932226	K562	blood:	n/a	n/a
34	ELF1	chr2:96931126-96932531	MCF-7	breast:	n/a	chr2:96931728-96931741 chr2:96931730-96931739 chr2:96931808-96931817 chr2:96931729-96931740 chr2:96931810-96931822
35	EGR1	chr2:96931448-96932244	MCF-7	breast:	n/a	chr2:96931729-96931738 chr2:96931823-96931847
36	ZBTB7A	chr2:96931009-96932351	K562	blood:	n/a	n/a
37	E2F4	chr2:96931713-96932298	GM12878	blood:	n/a	chr2:96931805-96931814
38	POLR2A	chr2:96931499-96932372	H1-hESC	embryonic stem cell:	n/a	n/a
39	ZBTB33	chr2:96931605-96932095	K562	blood:	n/a	chr2:96931854-96931869
40	USF2	chr2:96931720-96932528	Hela-S3	cervix:	n/a	n/a
41	GABPA	chr2:96931233-96932602	A549	lung:	n/a	chr2:96931783-96931792
42	POLR2A	chr2:96931368-96932361	PANC-1	pancreas:	n/a	n/a
43	SIX5	chr2:96931567-96932050	H1-hESC	embryonic stem cell:	n/a	n/a
44	HA-E2F1	chr2:96931596-96932385	Hela-S3	cervix:	n/a	chr2:96931805-96931814
45	MAX	chr2:96931609-96932519	A549	lung:	n/a	n/a
46	ELF1	chr2:96931399-96932187	A549	lung:	n/a	chr2:96931728-96931741 chr2:96931730-96931739 chr2:96931808-96931817 chr2:96931729-96931740 chr2:96931810-96931822
47	SIN3AK20	chr2:96931157-96932741	MCF-7	breast:	n/a	n/a
48	HMGN3	chr2:96930822-96932355	K562	blood:	n/a	n/a
49	SMC3	chr2:96931580-96932427	Hela-S3	cervix:	n/a	n/a
50	CBX3	chr2:96931534-96932580	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96923812..96929557-chr2:96929618..96934014,11	K562	blood:
2	chr2:96929992..96934856-chr2:96999935..97004454,8	K562	blood:
3	chr2:96871739..96877156-chr2:96928674..96935050,17	K562	blood:
4	chr2:96678462..96681368-chr2:96930331..96932535,2	K562	blood:
5	chr2:96929816..96932224-chr2:97173590..97175808,2	MCF-7	breast:
6	chr2:96930218..96933448-chr2:96968870..96972894,6	MCF-7	breast:
7	chr2:96930374..96934423-chr2:97000506..97002803,4	MCF-7	breast:
8	chr2:96868913..96876440-chr2:96928017..96934530,23	K562	blood:
9	chr2:96928652..96934635-chr2:96966746..96973769,11	K562	blood:
10	chr15:93425672..93426403-chr2:96931759..96932498,2	Hela-S3	cervix:
11	chr2:96930148..96938607-chr2:96966008..96973188,21	MCF-7	breast:
12	chr2:96812496..96814407-chr2:96931175..96932948,2	MCF-7	breast:
13	chr19:29703639..29704328-chr2:96931236..96932206,2	Hela-S3	cervix:
14	chr2:96871572..96876906-chr2:96928916..96935631,15	MCF-7	breast:
15	chr2:96929963..96932171-chr2:96999935..97002452,2	K562	blood:
16	chr2:96870309..96876262-chr2:96928720..96933891,16	MCF-7	breast:
17	chr2:96929774..96935946-chr2:96940519..96946631,7	K562	blood:
18	chr2:96809057..96813419-chr2:96930542..96933437,6	MCF-7	breast:
19	chr2:96930650..96934516-chr2:96954888..96957639,4	MCF-7	breast:
20	chr2:96931524..96933198-chr2:96984671..96987602,2	K562	blood:

Variant related genes	Relation type
CIAO1	TF binding region
TMEM127	TF binding region
ENSG00000144028	Chromatin interaction
ENSG00000272888	Chromatin interaction
ENSG00000230747	Chromatin interaction
ENSG00000121152	Chromatin interaction
ENSG00000158050	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000163121	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000267498	Chromatin interaction
ENSG00000228873	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000231584	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10183151	0.95[CEU][hapmap]
rs11680950	0.95[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs1168965	0.95[CEU][hapmap]
rs1168966	0.86[CEU][hapmap]
rs1168968	1.00[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs1168970	1.00[CEU][hapmap]
rs1168974	1.00[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs1168975	1.00[CEU][hapmap]
rs1168976	1.00[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs11693248	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13019188	0.80[CEU][hapmap]
rs1657502	0.82[CEU][hapmap]
rs2229169	0.95[CEU][hapmap]
rs2312955	0.90[CEU][hapmap]
rs2692893	0.86[CEU][hapmap]
rs2692894	0.95[CEU][hapmap]
rs2969490	0.86[CEU][hapmap]
rs2969491	0.95[CEU][hapmap]
rs3821051	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4426564	0.90[CEU][hapmap]
rs4907230	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4907299	0.90[CEU][hapmap]
rs58448550	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs749457	0.82[CEU][hapmap]
rs749459	0.82[CEU][hapmap]
rs7604842	0.95[CEU][hapmap]
rs772154	0.85[AMR][1000 genomes]
rs772175	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs772178	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs810057	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs893173	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2301707	GPAT2	cis	Muscle Skeletal	GTEx
rs2301707	ZNF2	cis	cerebellum	SCAN
rs2301707	ADRA2B	cis	Thyroid	GTEx
rs2301707	MRPL30	cis	parietal	SCAN
rs2301707	MGAT4A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96929800-96933200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr2:96930200-96932800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:96930200-96933000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:96930400-96932600	Active TSS	Lung	lung
5	chr2:96930400-96932800	Active TSS	Left Ventricle	heart
6	chr2:96930400-96932800	Active TSS	Ovary	ovary
7	chr2:96930400-96932800	Active TSS	Psoas Muscle	Psoas
8	chr2:96930400-96932800	Active TSS	Right Atrium	heart
9	chr2:96930400-96933000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:96930400-96933000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr2:96930400-96933000	Active TSS	GM12878-XiMat	blood
12	chr2:96930400-96933400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:96930600-96932200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:96930600-96932400	Active TSS	Primary hematopoietic stem cells	blood
15	chr2:96930600-96932600	Active TSS	Aorta	Aorta
16	chr2:96930600-96932800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr2:96930600-96932800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:96930600-96932800	Active TSS	Muscle Satellite Cultured Cells	--
19	chr2:96930600-96932800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:96930600-96932800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:96930600-96932800	Active TSS	Small Intestine	intestine
22	chr2:96930600-96933000	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr2:96930600-96933000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:96930600-96933000	Active TSS	Fetal Intestine Large	intestine
25	chr2:96930600-96933000	Active TSS	Fetal Intestine Small	intestine
26	chr2:96930600-96933000	Active TSS	NH-A	brain
27	chr2:96930600-96933200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:96930600-96933200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:96930600-96933200	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr2:96930800-96932200	Active TSS	Primary monocytes fromperipheralblood	blood
31	chr2:96930800-96932200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:96930800-96932200	Active TSS	Monocytes-CD14+_RO01746	blood
33	chr2:96930800-96932400	Active TSS	Primary T cells from cord blood	blood
34	chr2:96930800-96932400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:96930800-96932400	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr2:96930800-96932400	Active TSS	Fetal Heart	heart
37	chr2:96930800-96932400	Active TSS	Fetal Lung	lung
38	chr2:96930800-96932600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr2:96930800-96932600	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr2:96930800-96932600	Active TSS	Colon Smooth Muscle	Colon
41	chr2:96930800-96932600	Active TSS	Gastric	stomach
42	chr2:96930800-96932600	Active TSS	Stomach Mucosa	stomach
43	chr2:96930800-96932600	Active TSS	Thymus	Thymus
44	chr2:96930800-96932600	Active TSS	Spleen	Spleen
45	chr2:96930800-96932600	Bivalent/Poised TSS	HepG2	liver
46	chr2:96930800-96932800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:96930800-96932800	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr2:96930800-96932800	Active TSS	Brain Anterior Caudate	brain
49	chr2:96930800-96932800	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr2:96930800-96932800	Active TSS	Osteobl	bone

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