Variant report

Variant	rs10513002
Chromosome Location	chr3:136054982-136054983
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136044505..136047310-chr3:136053454..136056821,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10935178	1.00[CHB][hapmap]
rs13067714	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs16843978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843991	1.00[CHB][hapmap]
rs17199880	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17199978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17265675	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17266364	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	1.00[CHB][hapmap]
rs35644083	1.00[CHB][hapmap]
rs3872588	1.00[CHB][hapmap]
rs3913715	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4125861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55654524	0.81[EUR][1000 genomes]
rs56057807	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56095774	0.83[EUR][1000 genomes]
rs56264828	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336182	0.93[EUR][1000 genomes]
rs60270684	0.87[AMR][1000 genomes]
rs6439638	1.00[CHB][hapmap]
rs6439642	1.00[CHB][hapmap]
rs66494666	0.87[AMR][1000 genomes]
rs66637842	1.00[ASN][1000 genomes]
rs67230667	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67281610	0.87[AMR][1000 genomes]
rs67303976	0.87[AMR][1000 genomes]
rs67389407	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67452583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67525027	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67677899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67692166	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6769582	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs6773604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6776841	1.00[CHB][hapmap]
rs6783337	1.00[CHB][hapmap]
rs67963055	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67971203	0.87[EUR][1000 genomes]
rs6800570	1.00[CHB][hapmap]
rs6804194	1.00[CHB][hapmap]
rs6808143	0.92[EUR][1000 genomes]
rs72985474	0.82[AFR][1000 genomes]
rs73224201	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7625592	0.87[EUR][1000 genomes]
rs7650075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652176	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833162	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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4025	chr3:136017458-136065622	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10513002	TMEM22	cis	cerebellum	SCAN
rs10513002	STAG1	cis	cerebellum	SCAN
rs10513002	VCAN	trans	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
2	chr3:136032800-136055400	Weak transcription	HUVEC	blood vessel
3	chr3:136039000-136072400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:136039200-136062400	Weak transcription	Fetal Heart	heart
5	chr3:136040400-136062800	Weak transcription	Stomach Mucosa	stomach
6	chr3:136040600-136061400	Weak transcription	Small Intestine	intestine
7	chr3:136042400-136058200	Weak transcription	Psoas Muscle	Psoas
8	chr3:136042400-136078800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:136042600-136072600	Strong transcription	Dnd41	blood
10	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
11	chr3:136043600-136082000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:136043800-136070400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:136045200-136060800	Strong transcription	Liver	Liver
14	chr3:136045200-136062000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:136045600-136079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:136046200-136060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:136047800-136068200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:136047800-136074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:136048200-136060200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:136048400-136062800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:136048800-136062600	Weak transcription	NHEK	skin
23	chr3:136049000-136056000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:136049000-136062800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:136050800-136062800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:136051000-136062200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:136051000-136062400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:136051000-136062800	Strong transcription	Adipose Nuclei	Adipose
29	chr3:136051000-136063600	Strong transcription	Fetal Thymus	thymus
30	chr3:136051000-136069800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:136051200-136063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:136051400-136055000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:136051600-136055400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:136051600-136055600	Strong transcription	Fetal Intestine Small	intestine
35	chr3:136051600-136055600	Strong transcription	Fetal Stomach	stomach
36	chr3:136051600-136055600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:136051600-136055800	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:136051600-136057000	Strong transcription	GM12878-XiMat	blood
39	chr3:136051600-136063600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:136051600-136063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:136051600-136064800	Strong transcription	Primary T cells from cord blood	blood
42	chr3:136051600-136069200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:136051600-136070800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr3:136051800-136060400	Strong transcription	Fetal Brain Female	brain
45	chr3:136051800-136062400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr3:136052000-136055400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:136052000-136055600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:136052000-136055600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:136052000-136055600	Strong transcription	Brain Germinal Matrix	brain
50	chr3:136052000-136059600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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