Variant report

Variant	rs6717990
Chromosome Location	chr2:64371964-64371965
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	POLR2A	chr2:64370564-64372157	H1-hESC	embryonic stem cell:	n/a	n/a
2	EP300	chr2:64370940-64372816	ECC-1	luminal epithelium:	n/a	chr2:64371064-64371080 chr2:64371104-64371120 chr2:64371073-64371089 chr2:64371090-64371106 chr2:64371061-64371077
3	POLR2A	chr2:64370538-64371969	Hela-S3	cervix:	n/a	n/a
4	GABPA	chr2:64371231-64372034	MCF-7	breast:	n/a	chr2:64371735-64371749 chr2:64371590-64371599
5	ETS1	chr2:64371346-64372090	A549	lung:	n/a	chr2:64371664-64371677 chr2:64371587-64371598 chr2:64371752-64371761 chr2:64371588-64371599 chr2:64371663-64371676
6	POLR2A	chr2:64370819-64371985	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOXP2	chr2:64371474-64372008	SK-N-MC	brain:	n/a	n/a
8	RUNX3	chr2:64371121-64371966	GM12878	blood:	n/a	n/a
9	MAX	chr2:64370415-64371964	Hela-S3	cervix:	n/a	chr2:64371768-64371778 chr2:64371780-64371789
10	RAD21	chr2:64371347-64372028	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:64370889-64371997	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr2:64371257-64372076	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr2:64370360-64372030	H1-neurons	neurons:	n/a	n/a
14	ETS1	chr2:64371415-64372071	K562	blood:	n/a	chr2:64371664-64371677 chr2:64371587-64371598 chr2:64371752-64371761 chr2:64371588-64371599 chr2:64371663-64371676
15	IRF1	chr2:64371350-64372045	K562	blood:	n/a	chr2:64372028-64372037 chr2:64371589-64371603
16	CBX3	chr2:64371208-64372086	K562	blood:	n/a	n/a
17	RAD21	chr2:64371113-64371994	SK-N-SH_RA	brain:	n/a	n/a
18	SP1	chr2:64371497-64372002	H1-hESC	embryonic stem cell:	n/a	chr2:64371590-64371600 chr2:64371767-64371779 chr2:64371767-64371778 chr2:64371590-64371599 chr2:64371585-64371598 chr2:64371591-64371600 chr2:64371586-64371600 chr2:64371572-64371581 chr2:64371590-64371600 chr2:64371589-64371601 chr2:64371571-64371583 chr2:64371571-64371583 chr2:64371589-64371601 chr2:64371591-64371600
19	MXI1	chr2:64369673-64372181	GM12878	blood:	n/a	chr2:64371780-64371795
20	MTA3	chr2:64371141-64372141	GM12878	blood:	n/a	n/a
21	MAX	chr2:64371189-64372060	MCF-7	breast:	n/a	chr2:64371768-64371778 chr2:64371780-64371789
22	POLR2A	chr2:64371132-64371988	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:64371260-64372036	GM12891	blood:	n/a	n/a
24	MYC	chr2:64370867-64371980	K562	blood:	n/a	chr2:64371768-64371778 chr2:64371780-64371789
25	POLR2A	chr2:64371681-64372017	H1-hESC	embryonic stem cell:	n/a	n/a
26	TBP	chr2:64371297-64372094	HepG2	liver:	n/a	n/a
27	SP1	chr2:64371276-64372018	A549	lung:	n/a	chr2:64371590-64371600 chr2:64371767-64371779 chr2:64371767-64371778 chr2:64371590-64371599 chr2:64371585-64371598 chr2:64371591-64371600 chr2:64371586-64371600 chr2:64371572-64371581 chr2:64371590-64371600 chr2:64371589-64371601 chr2:64371571-64371583 chr2:64371571-64371583 chr2:64371589-64371601 chr2:64371591-64371600
28	YY1	chr2:64371322-64371989	SK-N-SH_RA	brain:	n/a	chr2:64371587-64371601 chr2:64371590-64371599
29	MXI1	chr2:64369317-64372440	SK-N-SH	brain:	n/a	chr2:64371780-64371795
30	POLR2A	chr2:64371112-64371970	K562	blood:	n/a	n/a
31	NRF1	chr2:64371542-64372018	H1-hESC	embryonic stem cell:	n/a	chr2:64371735-64371749 chr2:64371590-64371599
32	POLR2A	chr2:64371123-64372026	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr2:64370743-64372090	GM12892	blood:	n/a	n/a
34	POLR2A	chr2:64370935-64372028	K562	blood:	n/a	n/a
35	ELF1	chr2:64371238-64372085	HepG2	liver:	n/a	n/a
36	NFIC	chr2:64371307-64372102	HepG2	liver:	n/a	n/a
37	MAX	chr2:64371276-64371998	NB4	blood:	n/a	chr2:64371768-64371778 chr2:64371780-64371789
38	POLR2A	chr2:64371270-64371986	K562	blood:	n/a	n/a
39	EP300	chr2:64371367-64372012	GM12878	blood:	n/a	n/a
40	TBP	chr2:64370460-64372024	K562	blood:	n/a	n/a
41	PAX5	chr2:64371179-64372033	GM12878	blood:	n/a	n/a
42	TBP	chr2:64370805-64372019	H1-hESC	embryonic stem cell:	n/a	n/a
43	RUNX3	chr2:64371113-64372067	GM12878	blood:	n/a	n/a
44	SP1	chr2:64371200-64372029	A549	lung:	n/a	chr2:64371590-64371600 chr2:64371767-64371779 chr2:64371767-64371778 chr2:64371590-64371599 chr2:64371585-64371598 chr2:64371591-64371600 chr2:64371586-64371600 chr2:64371572-64371581 chr2:64371590-64371600 chr2:64371589-64371601 chr2:64371571-64371583 chr2:64371571-64371583 chr2:64371589-64371601 chr2:64371591-64371600
45	ZKSCAN1	chr2:64371312-64371975	Hela-S3	cervix:	n/a	n/a
46	ELF1	chr2:64371407-64372064	MCF-7	breast:	n/a	n/a
47	RCOR1	chr2:64371344-64372050	K562	blood:	n/a	n/a
48	POLR2A	chr2:64371133-64372023	GM12892	blood:	n/a	n/a
49	IRF1	chr2:64371336-64372071	K562	blood:	n/a	chr2:64372028-64372037 chr2:64371589-64371603
50	YY1	chr2:64371275-64371977	GM12878	blood:	n/a	chr2:64371587-64371601 chr2:64371590-64371599

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64371841..64374701-chr2:64382172..64383968,2	MCF-7	breast:

Variant related genes	Relation type
PELI1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10196884	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125990	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12612414	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34212947	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3919686	0.81[AMR][1000 genomes]
rs6712714	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717575	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6761890	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7601151	0.80[AMR][1000 genomes];0.85[EUR][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	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer 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	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	19 gene(s)	inside rSNPs	diseases
19	nsv1004899	chr2:64369300-64513607	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	nsv535769	chr2:64369300-64513607	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Strong 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	24 gene(s)	inside rSNPs	diseases
21	nsv1015084	chr2:64369734-64512286	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	esv3373290	chr2:64370073-64372621	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64367200-64372400	Active TSS	GM12878-XiMat	blood
2	chr2:64368200-64372000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr2:64368600-64372000	Active TSS	Brain Angular Gyrus	brain
4	chr2:64368800-64372000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:64368800-64372000	Active TSS	Right Ventricle	heart
6	chr2:64368800-64372200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:64369000-64372000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:64369000-64372000	Active TSS	Aorta	Aorta
9	chr2:64369000-64372000	Active TSS	Colonic Mucosa	Colon
10	chr2:64369000-64372000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr2:64369000-64372000	Active TSS	Fetal Intestine Small	intestine
12	chr2:64369000-64372000	Active TSS	Fetal Stomach	stomach
13	chr2:64369000-64372000	Active TSS	Psoas Muscle	Psoas
14	chr2:64369000-64372000	Active TSS	Rectal Smooth Muscle	rectum
15	chr2:64369000-64372000	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr2:64369000-64372000	Active TSS	NHLF	lung
17	chr2:64369000-64372200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:64369000-64372200	Active TSS	Duodenum Mucosa	Duodenum
19	chr2:64369200-64372000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr2:64369200-64372000	Active TSS	Brain Substantia Nigra	brain
21	chr2:64369200-64372000	Active TSS	Stomach Smooth Muscle	stomach
22	chr2:64369200-64372200	Active TSS	Colon Smooth Muscle	Colon
23	chr2:64369200-64372200	Active TSS	Osteobl	bone
24	chr2:64369400-64372000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:64369400-64372200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:64369400-64372200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:64369600-64372000	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr2:64369800-64372000	Active TSS	Fetal Lung	lung
29	chr2:64370000-64372000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:64370000-64372000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr2:64370000-64372000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:64370000-64372000	Active TSS	Fetal Muscle Trunk	muscle
33	chr2:64370200-64372000	Active TSS	Left Ventricle	heart
34	chr2:64370400-64372000	Active TSS	Esophagus	oesophagus
35	chr2:64370400-64372000	Active TSS	Fetal Brain Female	brain
36	chr2:64370400-64372200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:64370400-64372200	Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:64370400-64372600	Active TSS	Lung	lung
39	chr2:64370600-64372200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:64370800-64372000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:64370800-64372000	Active TSS	A549	lung
42	chr2:64371400-64372200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:64371600-64372000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr2:64371600-64372000	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr2:64371600-64372000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr2:64371600-64372000	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr2:64371600-64372000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:64371600-64372000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr2:64371600-64372000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr2:64371600-64372000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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