Variant report

Variant	rs2690102
Chromosome Location	chr6:25278627-25278628
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	KAP1	chr6:25278193-25279426	HEK293	kidney:	n/a	n/a
2	SMC3	chr6:25278594-25281162	Hela-S3	cervix:	n/a	chr6:25279245-25279259
3	GATA2	chr6:25278361-25279446	SH-SY5Y	brain:	n/a	chr6:25278424-25278440 chr6:25278422-25278443 chr6:25278429-25278436 chr6:25278429-25278436 chr6:25278429-25278436 chr6:25278644-25278654
4	RAD21	chr6:25278624-25281036	SK-N-SH	brain:	n/a	chr6:25279244-25279263 chr6:25279247-25279260 chr6:25279245-25279259
5	ZKSCAN1	chr6:25278622-25279028	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr6:25278554-25280596	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr6:25278481-25280742	SK-N-SH	brain:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
8	CHD2	chr6:25278538-25280897	Hela-S3	cervix:	n/a	chr6:25279278-25279288
9	ZNF263	chr6:25278178-25281125	HEK293-T-REx	kidney:	n/a	chr6:25280300-25280309 chr6:25278453-25278462
10	SMC3	chr6:25278534-25278693	GM12878	blood:	n/a	n/a
11	SMARCC1	chr6:25278460-25281460	Hela-S3	cervix:	n/a	n/a
12	SMC3	chr6:25277805-25281298	SK-N-SH	brain:	n/a	chr6:25279245-25279259
13	REST	chr6:25278540-25280544	H1-neurons	neurons:	n/a	chr6:25278554-25278574

No.	Distal block	Cell Line	Cell type
1	chr6:25277631..25279275-chr6:25301822..25304144,2	MCF-7	breast:
2	chr6:25277929..25281528-chr6:25281560..25287992,8	MCF-7	breast:
3	chr6:25277697..25280622-chr6:25286931..25288666,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213972	TF binding region
LRRC16A	TF binding region
ENSG00000207286	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1046141	1.00[CHD][hapmap]
rs11759648	1.00[CHD][hapmap]
rs11965121	1.00[TSI][hapmap]
rs16890271	1.00[ASN][1000 genomes]
rs1810471	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1815097	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880270	1.00[EUR][1000 genomes]
rs1880271	1.00[CHD][hapmap]
rs1900552	1.00[CHD][hapmap]
rs2044553	1.00[CHD][hapmap]
rs2328862	1.00[EUR][1000 genomes]
rs2328869	1.00[TSI][hapmap]
rs2690043	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690044	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690045	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690046	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690047	1.00[CHD][hapmap]
rs2690048	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690049	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690050	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690051	0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690052	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690055	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2690057	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2690058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690062	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690063	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2690066	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690069	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690073	0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690075	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690076	1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2690104	1.00[ASN][1000 genomes]
rs2690116	1.00[EUR][1000 genomes]
rs2690124	1.00[CHD][hapmap]
rs2744252	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744253	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744255	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744260	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744263	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744266	1.00[ASW][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744272	0.87[AFR][1000 genomes]
rs2744275	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744276	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744277	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744278	0.81[LWK][hapmap];0.97[MKK][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744279	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744280	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744282	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2744284	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2744285	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744286	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744291	1.00[EUR][1000 genomes]
rs2744292	1.00[EUR][1000 genomes]
rs34935689	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6456653	1.00[CHD][hapmap]
rs7739830	1.00[CHD][hapmap]
rs7743997	1.00[ASN][1000 genomes]
rs7755584	1.00[CHD][hapmap]
rs7767189	1.00[ASN][1000 genomes]
rs940405	1.00[ASW][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467496	1.00[CHD][hapmap]
rs9688905	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25278000-25278800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr6:25278000-25279000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:25278200-25278800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:25278200-25278800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:25278200-25278800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:25278200-25278800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:25278200-25278800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:25278200-25278800	Enhancers	Fetal Heart	heart
9	chr6:25278200-25278800	Enhancers	NH-A	brain
10	chr6:25278200-25279000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr6:25278200-25279000	Flanking Active TSS	Hela-S3	cervix
12	chr6:25278200-25279200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:25278400-25278800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:25278400-25278800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:25278400-25278800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:25278400-25278800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:25278400-25278800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:25278400-25278800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:25278400-25278800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:25278400-25278800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:25278400-25278800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:25278400-25278800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:25278400-25278800	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr6:25278400-25278800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr6:25278400-25278800	Flanking Active TSS	Fetal Brain Female	brain
26	chr6:25278400-25278800	Enhancers	Placenta	Placenta
27	chr6:25278400-25278800	Enhancers	Fetal Thymus	thymus
28	chr6:25278400-25278800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr6:25278400-25278800	Enhancers	NHLF	lung
30	chr6:25278400-25279000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:25278400-25279000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:25278400-25279000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:25278400-25279000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:25278400-25279000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:25278400-25279000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:25278400-25279000	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr6:25278400-25279000	Enhancers	Gastric	stomach
38	chr6:25278400-25279000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr6:25278400-25279000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr6:25278400-25279000	Enhancers	Spleen	Spleen
41	chr6:25278400-25279000	Flanking Active TSS	HMEC	breast
42	chr6:25278400-25279200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:25278400-25279200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr6:25278400-25279200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:25278400-25279200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:25278400-25279200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr6:25278400-25279200	Flanking Bivalent TSS/Enh	HepG2	liver
48	chr6:25278400-25279200	Flanking Active TSS	NHEK	skin
49	chr6:25278400-25280000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:25278400-25280800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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