Variant report

Variant	rs10929624
Chromosome Location	chr2:10079926-10079927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:9982989..9985362-chr2:10078538..10080122,2	MCF-7	breast:
2	chr2:10079779..10081937-chr2:10082992..10085179,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10803709	0.82[JPT][hapmap]
rs12468764	0.82[JPT][hapmap]
rs16867193	0.82[MEX][hapmap]
rs16867245	0.82[MEX][hapmap]
rs2052946	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288642	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357391	0.82[JPT][hapmap]
rs34577787	0.82[JPT][hapmap]
rs4668654	0.82[JPT][hapmap]
rs4669497	0.82[JPT][hapmap]
rs6721644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750872	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10929624	NTSR2	cis	parietal	SCAN
rs10929624	SERPINB4	trans	parietal	SCAN
rs10929624	TAF1B	cis	parietal	SCAN
rs10929624	TAF1B	cis	cerebellum	SCAN
rs10929624	GRHL1	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
5	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
8	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:10055200-10080800	Weak transcription	HMEC	breast
11	chr2:10059000-10080600	Weak transcription	HSMMtube	muscle
12	chr2:10059400-10081200	Weak transcription	GM12878-XiMat	blood
13	chr2:10060600-10080200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:10061000-10080800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:10061000-10080800	Weak transcription	NH-A	brain
16	chr2:10061000-10080800	Weak transcription	NHEK	skin
17	chr2:10062600-10080200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:10063000-10080800	Weak transcription	NHLF	lung
19	chr2:10064200-10080200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:10065000-10080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:10070800-10080800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:10073400-10081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:10073400-10084400	Weak transcription	Lung	lung
24	chr2:10073600-10088800	Weak transcription	Spleen	Spleen
25	chr2:10073800-10080000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:10073800-10080800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:10073800-10080800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:10073800-10081000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:10073800-10082000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:10074000-10081800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:10074200-10081800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:10074400-10080200	Weak transcription	HSMM	muscle
33	chr2:10074400-10080800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:10074800-10080000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:10075200-10080200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:10075600-10080000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:10075600-10080400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:10075600-10080800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:10075600-10080800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:10075600-10080800	Weak transcription	NHDF-Ad	bronchial
41	chr2:10075600-10082400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:10075800-10080200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:10075800-10080200	Weak transcription	Primary T cells from cord blood	blood
44	chr2:10075800-10080600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:10075800-10081200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:10075800-10081600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:10075800-10081600	Weak transcription	Placenta	Placenta
48	chr2:10076000-10081400	Weak transcription	Fetal Thymus	thymus
49	chr2:10076000-10081600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:10076200-10080000	Weak transcription	Thymus	Thymus

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