Variant report

Variant	rs10508929
Chromosome Location	chr10:52171981-52171982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52171539..52173257-chr10:52383288..52386072,2	MCF-7	breast:
2	chr10:52169460..52174968-chr10:52176430..52182227,8	K562	blood:
3	chr10:52165612..52167461-chr10:52171890..52173400,2	K562	blood:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10443954	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs10458673	0.91[ASN][1000 genomes]
rs10508926	0.86[YRI][hapmap]
rs10508927	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10508928	0.88[JPT][hapmap]
rs10733968	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10740684	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10763373	0.88[JPT][hapmap]
rs10763382	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10763392	0.92[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10763426	0.99[ASN][1000 genomes]
rs10763500	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10825789	0.88[JPT][hapmap]
rs10825859	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10825861	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10825882	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10825904	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10825934	0.99[ASN][1000 genomes]
rs10825978	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10825995	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10825996	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10826013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10826033	0.89[ASN][1000 genomes]
rs10826036	0.88[ASN][1000 genomes]
rs11005356	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11005399	0.88[JPT][hapmap]
rs11005418	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11005579	0.94[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs11005614	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11005621	0.97[ASN][1000 genomes]
rs11005761	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11005803	0.88[ASN][1000 genomes]
rs11005884	0.87[ASN][1000 genomes]
rs12217648	0.99[ASN][1000 genomes]
rs12219070	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12355439	0.86[YRI][hapmap]
rs12358247	0.93[YRI][hapmap]
rs12360058	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs1884572	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1916572	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2144863	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2273402	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2339400	0.92[CEU][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2339401	0.84[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2339503	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2339507	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34122137	0.98[ASN][1000 genomes]
rs3739989	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4935165	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4935711	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4935728	0.82[ASN][1000 genomes]
rs7074024	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7079881	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7086029	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7090807	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7092749	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs7093878	0.93[EUR][1000 genomes]
rs7094029	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7477280	0.93[YRI][hapmap]
rs768185	0.88[JPT][hapmap]
rs7896315	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7920818	0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7922802	0.83[JPT][hapmap]
rs910817	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs927047	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs927048	0.94[JPT][hapmap];0.84[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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' 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	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10508929	C10orf71	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52147000-52176600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
3	chr10:52157800-52172000	Weak transcription	Fetal Lung	lung
4	chr10:52157800-52173200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr10:52157800-52175400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr10:52157800-52176800	Weak transcription	Lung	lung
7	chr10:52158800-52172200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:52160800-52176800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr10:52163600-52176800	Weak transcription	Thymus	Thymus
10	chr10:52164400-52172400	Weak transcription	Ovary	ovary
11	chr10:52164400-52173800	Weak transcription	Psoas Muscle	Psoas
12	chr10:52164400-52174000	Weak transcription	Brain Angular Gyrus	brain
13	chr10:52164400-52177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr10:52164600-52176600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr10:52166600-52175800	Weak transcription	Primary T cells from cord blood	blood
16	chr10:52166600-52177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr10:52166800-52177200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr10:52166800-52177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr10:52167000-52176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr10:52167000-52176800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr10:52167000-52177200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr10:52167000-52177400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr10:52167600-52173000	Weak transcription	HepG2	liver
24	chr10:52167600-52176800	Weak transcription	Primary B cells from cord blood	blood
25	chr10:52168000-52177400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr10:52168600-52176200	Weak transcription	Right Atrium	heart
27	chr10:52168600-52176600	Weak transcription	Fetal Brain Male	brain
28	chr10:52169000-52172400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:52169600-52172200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr10:52169800-52172200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr10:52170000-52172000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:52170000-52172200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr10:52170000-52174200	Enhancers	Brain Substantia Nigra	brain
34	chr10:52170200-52172200	Weak transcription	A549	lung
35	chr10:52170200-52176400	Weak transcription	Small Intestine	intestine
36	chr10:52170200-52176800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr10:52170400-52175000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr10:52170400-52175000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:52170400-52175200	Enhancers	Hela-S3	cervix
40	chr10:52170400-52176200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr10:52170400-52176800	Weak transcription	Right Ventricle	heart
42	chr10:52170400-52178400	Active TSS	GM12878-XiMat	blood
43	chr10:52170600-52172000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr10:52170600-52172200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr10:52170600-52173200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr10:52170600-52174000	Weak transcription	Left Ventricle	heart
47	chr10:52170600-52175200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:52170600-52175200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr10:52170600-52175600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr10:52170600-52176200	Weak transcription	HMEC	breast

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