Variant report

Variant	rs10764641
Chromosome Location	chr10:27069902-27069903
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:27068463..27071008-chr10:27149449..27152029,3	K562	blood:
2	chr10:27064202..27066612-chr10:27068536..27071634,3	K562	blood:
3	chr10:27063322..27065877-chr10:27068617..27071382,2	K562	blood:
4	chr10:27067079..27070597-chr10:27072640..27074844,4	K562	blood:
5	chr10:27054901..27057514-chr10:27069095..27071711,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136754	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1031858	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741117	0.87[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10741119	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10741121	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10764638	0.92[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10764639	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10829063	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10829064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10829071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12221102	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1324637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1542553	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1543849	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1590445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998631	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998634	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2148110	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2182293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2368184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368185	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3916988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4376804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4747575	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4749185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6482575	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078119	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7078227	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895417	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7895559	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7907630	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915128	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv933544	chr10:27005220-27111998	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv6132	chr10:27066081-27075522	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10764641	WAC	cis	parietal	SCAN
rs10764641	LYZL2	cis	cerebellum	SCAN
rs10764641	MYO3A	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27023400-27070000	Weak transcription	Pancreas	Pancrea
2	chr10:27025800-27070800	Weak transcription	Aorta	Aorta
3	chr10:27044800-27070400	Weak transcription	HUVEC	blood vessel
4	chr10:27044800-27082000	Weak transcription	Fetal Lung	lung
5	chr10:27051400-27082000	Weak transcription	Fetal Stomach	stomach
6	chr10:27055600-27070200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:27057800-27072000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr10:27058000-27072200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:27058000-27079200	Weak transcription	Dnd41	blood
10	chr10:27064600-27074200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr10:27066200-27074600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr10:27066400-27074000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr10:27066400-27074600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr10:27066400-27075200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr10:27066600-27070600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:27066600-27071200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr10:27066800-27073400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:27067200-27073000	Enhancers	Primary B cells from peripheral blood	blood
19	chr10:27067400-27070000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr10:27067600-27072200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr10:27067800-27070400	Enhancers	Fetal Intestine Large	intestine
22	chr10:27067800-27071000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr10:27067800-27071200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr10:27067800-27071200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr10:27067800-27071400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr10:27068000-27070600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr10:27068000-27070800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr10:27068000-27071200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr10:27068200-27070000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:27068200-27070000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:27068200-27070400	Enhancers	HMEC	breast
32	chr10:27068200-27070600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr10:27068200-27071000	Flanking Active TSS	GM12878-XiMat	blood
34	chr10:27068200-27071200	Enhancers	Stomach Mucosa	stomach
35	chr10:27068200-27071200	Enhancers	Spleen	Spleen
36	chr10:27068200-27072000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:27068400-27070000	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr10:27068400-27070000	Enhancers	A549	lung
39	chr10:27068400-27070400	Enhancers	Thymus	Thymus
40	chr10:27068400-27071000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:27068400-27071200	Enhancers	Duodenum Mucosa	Duodenum
42	chr10:27068400-27071200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr10:27068400-27071800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr10:27068400-27072000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr10:27068400-27079400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr10:27068600-27070000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr10:27068600-27071000	Enhancers	Fetal Intestine Small	intestine
48	chr10:27068600-27071200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr10:27068600-27073000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:27068600-27074200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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