Variant report

Variant	rs12259474
Chromosome Location	chr10:94366898-94366899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:94352566..94354607-chr10:94365901..94367926,3	MCF-7	breast:
2	chr10:94362820..94365459-chr10:94365788..94367385,2	K562	blood:

Variant related genes	Relation type
ENSG00000138160	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11187083	0.99[AFR][1000 genomes]
rs11187084	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187087	0.98[AFR][1000 genomes]
rs11187100	0.93[AFR][1000 genomes]
rs11187102	0.98[AFR][1000 genomes]
rs11187104	0.98[AFR][1000 genomes]
rs11187120	0.91[AFR][1000 genomes]
rs11812310	0.99[AFR][1000 genomes]
rs11812813	0.91[AFR][1000 genomes]
rs11816962	0.96[AFR][1000 genomes]
rs11817621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11817798	0.99[AFR][1000 genomes]
rs11818332	0.99[AFR][1000 genomes]
rs11818705	0.80[AFR][1000 genomes]
rs11818708	0.87[AFR][1000 genomes]
rs11818750	0.96[AFR][1000 genomes]
rs11819301	0.96[AFR][1000 genomes]
rs11819351	0.98[AFR][1000 genomes]
rs12242681	0.99[AFR][1000 genomes]
rs12244573	0.98[AFR][1000 genomes]
rs12244660	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244738	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244809	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244924	0.98[AFR][1000 genomes]
rs12246900	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12250905	0.99[AFR][1000 genomes]
rs12252642	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12257279	0.99[AFR][1000 genomes]
rs12260688	0.98[AFR][1000 genomes]
rs12261518	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261697	0.89[AFR][1000 genomes]
rs12262350	1.00[ASN][1000 genomes]
rs12262781	0.96[AFR][1000 genomes]
rs12264372	0.98[AFR][1000 genomes]
rs12264712	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12779070	0.83[EUR][1000 genomes]
rs17107758	0.99[AFR][1000 genomes]
rs17107764	0.98[AFR][1000 genomes]
rs17875340	0.98[AFR][1000 genomes]
rs2488057	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488058	0.85[AFR][1000 genomes]
rs2497319	0.86[AFR][1000 genomes]
rs2497320	0.86[AFR][1000 genomes]
rs2497321	1.00[ASN][1000 genomes]
rs28615450	0.96[AFR][1000 genomes]
rs28692618	0.98[AFR][1000 genomes]
rs3781236	0.99[AFR][1000 genomes]
rs4604791	0.99[AFR][1000 genomes]
rs58071219	0.99[AFR][1000 genomes]
rs58177786	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58988864	0.99[AFR][1000 genomes]
rs61011943	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6583828	0.83[AFR][1000 genomes]
rs6583829	0.98[AFR][1000 genomes]
rs6583832	0.96[AFR][1000 genomes]
rs6583834	0.85[AFR][1000 genomes]
rs6583837	0.86[AFR][1000 genomes]
rs7068540	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073739	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073868	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7076842	0.86[AFR][1000 genomes]
rs7079602	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082683	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084441	0.98[AFR][1000 genomes]
rs7085790	0.92[AFR][1000 genomes]
rs7087860	0.98[AFR][1000 genomes]
rs7088685	0.96[AFR][1000 genomes]
rs7095585	0.83[AFR][1000 genomes]
rs7096520	0.91[AFR][1000 genomes]
rs7100344	1.00[ASN][1000 genomes]
rs73311731	0.86[AFR][1000 genomes]
rs73325674	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73325701	0.98[AFR][1000 genomes]
rs7898478	0.82[AFR][1000 genomes]
rs7898506	0.98[AFR][1000 genomes]
rs7902436	0.86[AFR][1000 genomes]
rs7914248	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915915	0.96[AFR][1000 genomes]
rs7917359	0.88[AFR][1000 genomes]
rs7922902	0.96[AFR][1000 genomes]
rs9731595	0.92[AFR][1000 genomes]

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	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	esv1792868	chr10:94232247-94409749	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv895894	chr10:94249982-94452430	Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv895895	chr10:94304132-94372706	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94353600-94403800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:94354000-94372000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:94354000-94420000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:94354200-94369000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:94354200-94416000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:94354800-94373400	Weak transcription	Fetal Intestine Small	intestine
7	chr10:94355000-94368200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr10:94355000-94372200	Weak transcription	HSMM	muscle
9	chr10:94355200-94372000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:94355600-94368400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:94355800-94369000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:94355800-94369200	Weak transcription	NH-A	brain
13	chr10:94355800-94369400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr10:94356000-94367600	Weak transcription	Fetal Stomach	stomach
15	chr10:94356800-94385600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:94357000-94367200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr10:94358600-94372200	Weak transcription	K562	blood
18	chr10:94361800-94372600	Weak transcription	NHEK	skin
19	chr10:94362000-94372600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:94362000-94372600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr10:94362000-94381200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:94362000-94389400	Weak transcription	NHLF	lung
23	chr10:94362000-94399800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:94362400-94368600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:94362400-94371800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr10:94362600-94367000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr10:94362600-94376400	Weak transcription	Fetal Lung	lung
28	chr10:94362800-94372200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr10:94363600-94410200	Weak transcription	Fetal Kidney	kidney
30	chr10:94364000-94390600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr10:94364000-94416400	Strong transcription	Dnd41	blood
32	chr10:94364200-94417400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr10:94364400-94368400	Weak transcription	HMEC	breast
34	chr10:94364400-94403800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:94364400-94415200	Weak transcription	Fetal Heart	heart
36	chr10:94364600-94367000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr10:94364600-94369200	Weak transcription	Osteobl	bone
38	chr10:94364800-94368400	Weak transcription	NHDF-Ad	bronchial
39	chr10:94364800-94383600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:94365000-94368600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr10:94365000-94372000	Weak transcription	Thymus	Thymus
42	chr10:94365000-94385400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:94365000-94395200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr10:94365200-94371200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:94365200-94372200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr10:94365600-94367400	Strong transcription	GM12878-XiMat	blood
47	chr10:94365600-94369400	Strong transcription	HUVEC	blood vessel
48	chr10:94365600-94379400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr10:94365600-94390600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr10:94365600-94415600	Strong transcription	Fetal Thymus	thymus

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