Variant report

Variant	rs7599656
Chromosome Location	chr2:86265621-86265622
allele	G/T
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	POLR2A	chr2:86265359-86265811	PFSK-1	brain:	n/a	n/a
2	ZNF263	chr2:86265343-86265683	HEK293-T-REx	kidney:	n/a	n/a
3	POLR2A	chr2:86265272-86266252	HL-60	blood:	n/a	n/a
4	SPI1	chr2:86265522-86266031	GM12891	blood:	n/a	n/a
5	RCOR1	chr2:86262772-86265905	IMR90	lung:	n/a	n/a
6	MAX	chr2:86265115-86265724	GM12878	blood:	n/a	n/a
7	BRCA1	chr2:86265499-86265699	GM12878	blood:	n/a	n/a
8	EBF1	chr2:86265480-86265729	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:86265284-86266180	GM12878	blood:	n/a	n/a
10	EP300	chr2:86264991-86265935	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr2:86265400-86265746	GM12878	blood:	n/a	n/a
12	EP300	chr2:86265358-86265786	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:86265334-86266141	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr2:86265402-86265888	HepG2	liver:	n/a	n/a
15	MTA3	chr2:86265509-86266028	GM12878	blood:	n/a	n/a
16	EP300	chr2:86265324-86266114	GM12878	blood:	n/a	n/a
17	RELA	chr2:86265011-86266158	GM19099	blood:	n/a	n/a
18	WRNIP1	chr2:86265007-86266068	GM12878	blood:	n/a	n/a
19	RCOR1	chr2:86264929-86265843	GM12878	blood:	n/a	n/a
20	POU2F2	chr2:86265214-86266114	GM12878	blood:	n/a	n/a
21	RUNX3	chr2:86265341-86266239	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:86265363-86265682	HepG2	liver:	n/a	n/a
23	IKZF1	chr2:86265434-86265962	GM12878	blood:	n/a	n/a
24	CHD2	chr2:86265053-86265868	GM12878	blood:	n/a	n/a
25	BHLHE40	chr2:86265032-86265761	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:86265304-86266620	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86263075..86266284-chr2:86266783..86270779,4	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2278086	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes]
rs2278088	0.85[LWK][hapmap]
rs2278537	1.00[AFR][1000 genomes]
rs34302587	0.93[AFR][1000 genomes]
rs35093541	0.96[AFR][1000 genomes]
rs36051710	0.96[AFR][1000 genomes]
rs3731822	1.00[ASW][hapmap];1.00[TSI][hapmap]
rs3770086	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3770091	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs56673339	1.00[AFR][1000 genomes]
rs57906735	1.00[AFR][1000 genomes]
rs58403969	1.00[AFR][1000 genomes]
rs58614836	0.89[AFR][1000 genomes]
rs59947468	0.90[AFR][1000 genomes]
rs60719866	0.96[AFR][1000 genomes]
rs60887312	0.83[AFR][1000 genomes]
rs61185790	1.00[AFR][1000 genomes]
rs6547656	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6547657	1.00[AFR][1000 genomes]
rs6704777	1.00[AFR][1000 genomes]
rs6708146	1.00[AFR][1000 genomes]
rs6712535	1.00[AFR][1000 genomes]
rs6712576	1.00[AFR][1000 genomes]
rs6724612	0.93[AFR][1000 genomes]
rs6737211	1.00[AFR][1000 genomes]
rs6741815	1.00[AFR][1000 genomes]
rs6741832	1.00[AFR][1000 genomes]
rs6755224	1.00[AFR][1000 genomes]
rs6755246	0.96[AFR][1000 genomes]
rs7557349	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7569577	1.00[AFR][1000 genomes]
rs7572206	1.00[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7582484	1.00[AFR][1000 genomes]
rs7606062	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr2:86251200-86283000	Strong transcription	HepG2	liver
4	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:86252600-86267800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:86260200-86266200	Genic enhancers	Fetal Stomach	stomach
14	chr2:86260600-86268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:86260600-86269000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:86260800-86268800	Weak transcription	Ovary	ovary
17	chr2:86261200-86272000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:86261400-86266200	Enhancers	Psoas Muscle	Psoas
19	chr2:86261800-86266400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:86262000-86265800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:86262400-86266000	Genic enhancers	Brain Angular Gyrus	brain
22	chr2:86262400-86266000	Genic enhancers	Fetal Intestine Small	intestine
23	chr2:86262400-86266000	Enhancers	Right Atrium	heart
24	chr2:86262400-86266200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:86262400-86266200	Enhancers	Lung	lung
26	chr2:86262400-86266800	Genic enhancers	Placenta	Placenta
27	chr2:86262400-86268400	Flanking Active TSS	Thymus	Thymus
28	chr2:86262600-86265800	Enhancers	Colon Smooth Muscle	Colon
29	chr2:86262600-86265800	Enhancers	Small Intestine	intestine
30	chr2:86262600-86266200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:86262600-86266200	Enhancers	Stomach Mucosa	stomach
32	chr2:86262600-86266200	Genic enhancers	NHLF	lung
33	chr2:86262600-86267000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr2:86262800-86266000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:86263000-86266000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:86263600-86266400	Enhancers	Primary hematopoietic stem cells	blood
37	chr2:86263600-86266400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:86263600-86266400	Genic enhancers	Rectal Mucosa Donor 31	rectum
39	chr2:86263800-86266400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:86263800-86267200	Enhancers	Primary B cells from peripheral blood	blood
41	chr2:86263800-86268000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:86263800-86268800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:86263800-86269200	Enhancers	Primary T cells fromperipheralblood	blood
44	chr2:86264000-86265800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:86264000-86266600	Genic enhancers	HSMM	muscle
46	chr2:86264000-86268200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr2:86264000-86269000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:86264000-86281800	Strong transcription	Fetal Brain Female	brain
49	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:86264200-86267200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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