Variant report

Variant	rs6959558
Chromosome Location	chr7:6512050-6512051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:6511092-6518405	IMR90	lung:	n/a	n/a
2	POLR2A	chr7:6511657-6512473	HepG2	liver:	n/a	n/a
3	PML	chr7:6511980-6512457	K562	blood:	n/a	n/a
4	POLR2A	chr7:6511778-6512248	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr7:6511817-6512153	K562	blood:	n/a	n/a
6	POLR2A	chr7:6511800-6512299	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:6510963-6513188	GM12892	blood:	n/a	n/a
8	POLR2A	chr7:6511747-6512190	K562	blood:	n/a	n/a
9	POLR2A	chr7:6511949-6512874	HepG2	liver:	n/a	n/a
10	MAFK	chr7:6511903-6512173	HepG2	liver:	n/a	n/a
11	POLR2A	chr7:6511123-6513118	A549	lung:	n/a	n/a
12	POLR2A	chr7:6511856-6512507	K562	blood:	n/a	n/a
13	POLR2A	chr7:6511656-6512385	GM12892	blood:	n/a	n/a
14	POLR2A	chr7:6511810-6512191	GM12891	blood:	n/a	n/a
15	BRCA1	chr7:6511928-6512109	HepG2	liver:	n/a	n/a
16	POLR2A	chr7:6511643-6512627	K562	blood:	n/a	n/a
17	POLR2A	chr7:6511823-6512237	GM12892	blood:	n/a	n/a
18	CHD2	chr7:6511946-6512141	HepG2	liver:	n/a	n/a
19	POLR2A	chr7:6511632-6513177	GM12891	blood:	n/a	n/a
20	POLR2A	chr7:6510984-6513437	K562	blood:	n/a	n/a
21	POLR2A	chr7:6511760-6512154	K562	blood:	n/a	n/a
22	POLR2A	chr7:6510893-6513146	GM12878	blood:	n/a	n/a
23	POLR2A	chr7:6511170-6513484	HepG2	liver:	n/a	n/a
24	POLR2A	chr7:6511591-6513174	GM12892	blood:	n/a	n/a
25	POLR2A	chr7:6511755-6512718	GM12891	blood:	n/a	n/a
26	BCL3	chr7:6511732-6512603	K562	blood:	n/a	n/a
27	POLR2A	chr7:6511705-6512121	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr7:6511727-6512173	GM12878	blood:	n/a	n/a
29	POLR2A	chr7:6510981-6512830	GM12891	blood:	n/a	n/a
30	POLR2A	chr7:6512021-6512252	HepG2	liver:	n/a	n/a
31	POLR2A	chr7:6511024-6519040	HepG2	liver:	n/a	n/a
32	POLR2A	chr7:6511833-6512311	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6509730..6517655-chr7:6520090..6524473,18	K562	blood:
2	chr7:6509433..6511485-chr7:6511518..6513143,2	MCF-7	breast:
3	chr7:6510413..6513811-chr7:6516009..6519454,4	MCF-7	breast:
4	chr7:6499717..6507603-chr7:6511410..6517764,12	K562	blood:
5	chr7:6503445..6506169-chr7:6511956..6514111,2	K562	blood:

No data

Variant related genes	Relation type
KDELR2	TF binding region
ENSG00000269781	Chromatin interaction
ENSG00000136240	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10951986	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes]
rs11766121	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12113949	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13233173	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes]
rs13239407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403782	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523609	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs2230263	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2347780	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881722	0.92[ASN][1000 genomes]
rs4720677	0.84[AMR][1000 genomes]
rs4724811	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs4724812	0.83[EUR][1000 genomes]
rs4724813	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58885063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463560	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6463561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6463562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463564	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs6463567	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6463568	0.89[AMR][1000 genomes]
rs6945009	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6953782	0.87[EUR][1000 genomes]
rs6959389	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959768	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6960903	0.85[AMR][1000 genomes]
rs6961571	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs6964421	0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7456862	0.82[EUR][1000 genomes]
rs7782950	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7788091	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs7796667	0.84[EUR][1000 genomes]
rs7799479	0.87[AMR][1000 genomes]
rs7800342	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs940243	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1026878	chr7:6490387-6592374	Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6497800-6515600	Weak transcription	Psoas Muscle	Psoas
2	chr7:6499600-6515200	Strong transcription	Fetal Intestine Large	intestine
3	chr7:6499600-6516200	Strong transcription	Fetal Stomach	stomach
4	chr7:6499600-6521800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:6499800-6513400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:6499800-6513400	Strong transcription	Brain Inferior Temporal Lobe	brain
7	chr7:6499800-6513800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:6499800-6513800	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr7:6499800-6514800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:6499800-6515600	Strong transcription	NH-A	brain
11	chr7:6499800-6517000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:6500000-6513000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:6500000-6513600	Strong transcription	Adipose Nuclei	Adipose
14	chr7:6500000-6514600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:6500000-6515000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr7:6500000-6515400	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr7:6500000-6515400	Strong transcription	HUVEC	blood vessel
18	chr7:6500000-6516000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:6500000-6516200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr7:6500000-6516400	Strong transcription	Fetal Thymus	thymus
21	chr7:6500200-6513200	Strong transcription	Ovary	ovary
22	chr7:6500200-6514000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:6500200-6515200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:6500200-6515400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr7:6500200-6516200	Strong transcription	Placenta	Placenta
26	chr7:6500200-6516400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:6500400-6514000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:6500400-6514200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr7:6500600-6513200	Strong transcription	Left Ventricle	heart
30	chr7:6500800-6513800	Strong transcription	Colonic Mucosa	Colon
31	chr7:6500800-6514600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:6500800-6517000	Strong transcription	Dnd41	blood
33	chr7:6501200-6513400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:6501200-6513600	Strong transcription	Fetal Lung	lung
35	chr7:6501200-6513800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr7:6501200-6516000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr7:6501400-6515000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr7:6501800-6514400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:6502200-6513200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:6502800-6515200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:6503600-6515600	Strong transcription	Osteobl	bone
42	chr7:6503600-6522800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr7:6504800-6514200	Strong transcription	HepG2	liver
44	chr7:6505000-6513200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr7:6505000-6514000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr7:6505000-6514000	Strong transcription	Liver	Liver
47	chr7:6505000-6514000	Strong transcription	Brain Hippocampus Middle	brain
48	chr7:6505000-6514200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:6505000-6514600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:6505000-6514800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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