Variant report

Variant	rs7089882
Chromosome Location	chr10:52357156-52357157
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52337504..52339571-chr10:52355930..52358209,2	K562	blood:
2	chr10:52355521..52357816-chr10:52359729..52362613,2	MCF-7	breast:
3	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:
4	chr10:52337504..52344093-chr10:52356709..52361052,9	K562	blood:
5	chr10:52355890..52357907-chr10:52372209..52373860,2	K562	blood:
6	chr10:52338640..52342298-chr10:52355605..52360278,4	MCF-7	breast:
7	chr10:52356255..52358116-chr10:52383809..52386039,2	MCF-7	breast:
8	chr10:52355970..52358426-chr10:52377071..52379971,2	K562	blood:
9	chr10:52356946..52359627-chr10:52382756..52385270,2	K562	blood:
10	chr10:52351092..52355625-chr10:52355822..52361152,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10740762	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs10763590	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs10825904	1.00[YRI][hapmap]
rs10825978	1.00[YRI][hapmap]
rs10826169	1.00[YRI][hapmap]
rs10826242	0.92[EUR][1000 genomes]
rs11005614	1.00[YRI][hapmap]
rs11006054	1.00[YRI][hapmap]
rs11006281	0.92[ASN][1000 genomes]
rs12219692	1.00[YRI][hapmap]
rs17497064	0.87[ASN][1000 genomes]
rs1916572	1.00[YRI][hapmap]
rs3001879	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3001883	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3001885	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3011714	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4268459	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4519042	0.82[ASN][1000 genomes]
rs4519043	0.81[ASN][1000 genomes]
rs4935735	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4935736	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs4935737	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4935739	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6481442	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6481461	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7067552	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7073182	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7086029	1.00[YRI][hapmap]
rs7090996	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7094655	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7097359	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7903649	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7904101	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7908136	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7909486	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7918559	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs927048	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv8661	chr10:52356909-52360389	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7089882	FLJ31958	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52336800-52363000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:52338000-52363800	Weak transcription	Fetal Kidney	kidney
3	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
4	chr10:52340400-52360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:52341400-52360200	Weak transcription	GM12878-XiMat	blood
7	chr10:52341800-52362000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:52342800-52360200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr10:52343400-52360600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:52343600-52362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:52343800-52360000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:52346400-52358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr10:52346600-52363400	Weak transcription	Adipose Nuclei	Adipose
14	chr10:52346600-52363800	Weak transcription	Spleen	Spleen
15	chr10:52346800-52360600	Weak transcription	HUVEC	blood vessel
16	chr10:52347000-52359600	Weak transcription	A549	lung
17	chr10:52348000-52363400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr10:52348200-52358400	Weak transcription	HepG2	liver
19	chr10:52348200-52360000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr10:52348400-52363000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr10:52349000-52363200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr10:52349200-52360400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr10:52349200-52363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr10:52349400-52358600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr10:52349400-52363000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:52349400-52363000	Weak transcription	Lung	lung
27	chr10:52349600-52358400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr10:52349600-52359200	Weak transcription	Placenta	Placenta
29	chr10:52349600-52360000	Weak transcription	Fetal Intestine Large	intestine
30	chr10:52349600-52360200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:52349600-52360200	Weak transcription	Fetal Intestine Small	intestine
32	chr10:52349600-52360200	Weak transcription	Fetal Muscle Leg	muscle
33	chr10:52349600-52360200	Weak transcription	Fetal Thymus	thymus
34	chr10:52349600-52360600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr10:52349600-52360600	Weak transcription	Thymus	Thymus
36	chr10:52349600-52361800	Weak transcription	Esophagus	oesophagus
37	chr10:52349600-52363600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr10:52349600-52364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:52349600-52364800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr10:52349800-52362600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr10:52349800-52362600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr10:52349800-52362800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:52349800-52363000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr10:52349800-52363800	Weak transcription	Primary B cells from cord blood	blood
45	chr10:52350000-52360000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr10:52350000-52360000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr10:52350000-52360400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr10:52350000-52360600	Weak transcription	Primary T cells from cord blood	blood
49	chr10:52351000-52359400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr10:52352400-52358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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