Variant report

Variant	rs10245008
Chromosome Location	chr7:101513404-101513405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:101459336..101463472-chr7:101510229..101514118,3	K562	blood:
2	chr7:101511680..101514939-chr7:101582566..101587455,5	MCF-7	breast:
3	chr7:101508293..101510760-chr7:101510780..101514938,6	K562	blood:
4	chr7:101513034..101514774-chr7:101650619..101652950,2	MCF-7	breast:
5	chr7:101512493..101515121-chr7:101518914..101521779,2	MCF-7	breast:
6	chr7:101506592..101509232-chr7:101513359..101515951,2	MCF-7	breast:
7	chr7:101506275..101507892-chr7:101511497..101513888,2	K562	blood:
8	chr7:101512988..101516254-chr7:101522807..101526538,9	MCF-7	breast:
9	chr7:101487333..101490087-chr7:101511385..101514324,2	K562	blood:
10	chr7:101513234..101515852-chr7:101521619..101524007,2	MCF-7	breast:
11	chr7:101512598..101514582-chr7:101516207..101518095,2	K562	blood:
12	chr7:101511316..101513776-chr7:101520159..101522862,2	K562	blood:
13	chr7:101459336..101461034-chr7:101512323..101514118,2	K562	blood:
14	chr7:101350597..101352580-chr7:101511716..101513955,2	K562	blood:
15	chr7:101512554..101516171-chr7:101524650..101528130,5	MCF-7	breast:
16	chr7:101512083..101520283-chr7:101521327..101527237,12	K562	blood:
17	chr7:101457997..101461675-chr7:101512950..101515695,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10224064	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10229003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261568	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10266326	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768899	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2970497	0.85[ASN][1000 genomes]
rs4236559	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs4727511	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4729755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729758	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6465836	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs6957294	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6978555	0.81[ASN][1000 genomes]
rs6979596	0.85[ASN][1000 genomes]
rs7803747	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10245008	CPSF4	cis	cerebellum	SCAN
rs10245008	ZKSCAN5	cis	parietal	SCAN
rs10245008	ARPC1B	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101501000-101517600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr7:101501000-101523600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:101501000-101525000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:101503400-101517400	Weak transcription	Primary B cells from cord blood	blood
5	chr7:101504800-101518200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr7:101509000-101513600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:101509000-101522600	Weak transcription	Primary T cells from cord blood	blood
8	chr7:101509200-101517200	Weak transcription	Dnd41	blood
9	chr7:101509200-101517200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr7:101509800-101514000	Enhancers	Fetal Thymus	thymus
11	chr7:101510000-101514400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr7:101510600-101513800	Enhancers	A549	lung
13	chr7:101510600-101514800	Enhancers	Lung	lung
14	chr7:101510600-101515000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr7:101510600-101515000	Enhancers	Pancreas	Pancrea
16	chr7:101510600-101515000	Enhancers	Right Ventricle	heart
17	chr7:101510800-101514400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:101511000-101514600	Enhancers	Thymus	Thymus
19	chr7:101511200-101514600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:101511400-101513600	Enhancers	Psoas Muscle	Psoas
21	chr7:101511400-101513800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr7:101511400-101513800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:101511400-101513800	Enhancers	Fetal Muscle Leg	muscle
24	chr7:101511400-101514400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr7:101511400-101514400	Enhancers	Colon Smooth Muscle	Colon
26	chr7:101511400-101514600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr7:101511400-101514800	Enhancers	Fetal Intestine Large	intestine
28	chr7:101511400-101514800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr7:101511400-101515000	Enhancers	Fetal Heart	heart
30	chr7:101511400-101515000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr7:101511400-101515000	Enhancers	K562	blood
32	chr7:101511400-101515200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr7:101511600-101513600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:101511600-101514200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr7:101511600-101514400	Enhancers	Stomach Smooth Muscle	stomach
36	chr7:101511600-101514600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr7:101511600-101514600	Enhancers	Left Ventricle	heart
38	chr7:101511600-101519000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:101511600-101523400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr7:101511800-101513600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:101511800-101514200	Enhancers	Stomach Mucosa	stomach
42	chr7:101511800-101514400	Enhancers	GM12878-XiMat	blood
43	chr7:101511800-101514800	Enhancers	Colonic Mucosa	Colon
44	chr7:101511800-101514800	Enhancers	Esophagus	oesophagus
45	chr7:101511800-101515000	Enhancers	H9 Cell Line	embryonic stem cell
46	chr7:101511800-101515000	Enhancers	Placenta	Placenta
47	chr7:101511800-101523600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:101512000-101513800	Enhancers	Hela-S3	cervix
49	chr7:101512000-101514200	Enhancers	Duodenum Mucosa	Duodenum
50	chr7:101512200-101513600	Enhancers	Rectal Mucosa Donor 29	rectum

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