Variant report

Variant	rs12258487
Chromosome Location	chr10:94290766-94290767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:94286303..94289350-chr10:94289651..94292347,3	MCF-7	breast:
2	chr10:94290717..94292368-chr10:94351080..94353916,2	K562	blood:
3	chr10:94289161..94292138-chr10:94332581..94334284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119912	Chromatin interaction
ENSG00000138160	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11187066	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252447	0.87[AFR][1000 genomes]
rs12253177	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12255048	0.89[AFR][1000 genomes]
rs12262994	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266443	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875329	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875332	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875344	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875345	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875346	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875347	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275218	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2275220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737225	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57299222	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74151654	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74151656	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74151657	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74151659	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74151667	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74151672	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909487	0.96[YRI][hapmap];0.84[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	esv1802816	chr10:94232247-94294291	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	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
4	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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94244000-94303000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:94250200-94295200	Weak transcription	Pancreas	Pancrea
3	chr10:94250200-94297200	Weak transcription	Brain Germinal Matrix	brain
4	chr10:94250200-94313800	Weak transcription	Brain Substantia Nigra	brain
5	chr10:94250400-94301000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr10:94250400-94307400	Weak transcription	Spleen	Spleen
7	chr10:94252600-94302200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:94260000-94296800	Weak transcription	Esophagus	oesophagus
9	chr10:94262000-94297600	Weak transcription	Psoas Muscle	Psoas
10	chr10:94262000-94307400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:94264200-94295000	Weak transcription	Small Intestine	intestine
12	chr10:94267600-94297400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:94267600-94314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:94267800-94328800	Weak transcription	Fetal Heart	heart
15	chr10:94268000-94313800	Weak transcription	Colon Smooth Muscle	Colon
16	chr10:94268000-94313800	Weak transcription	NHLF	lung
17	chr10:94268600-94290800	Weak transcription	Fetal Lung	lung
18	chr10:94268600-94295200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr10:94268600-94300000	Weak transcription	Colonic Mucosa	Colon
20	chr10:94269400-94314000	Weak transcription	Aorta	Aorta
21	chr10:94269600-94314000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:94269800-94295000	Weak transcription	Lung	lung
23	chr10:94272000-94317200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr10:94272200-94291000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr10:94272200-94298600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr10:94272200-94313800	Weak transcription	HSMMtube	muscle
27	chr10:94272200-94332000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:94272200-94332200	Weak transcription	Gastric	stomach
29	chr10:94272400-94293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr10:94272400-94313600	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:94272800-94291000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr10:94272800-94313200	Weak transcription	Fetal Brain Female	brain
33	chr10:94274400-94303400	Weak transcription	HMEC	breast
34	chr10:94274800-94292400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr10:94276800-94294400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:94276800-94304000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr10:94277000-94304000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr10:94277200-94298000	Weak transcription	Brain Anterior Caudate	brain
39	chr10:94277200-94303000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr10:94277200-94304000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr10:94277200-94313800	Weak transcription	Brain Angular Gyrus	brain
42	chr10:94277200-94331200	Weak transcription	Stomach Mucosa	stomach
43	chr10:94277400-94304200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:94277800-94332200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr10:94279400-94290800	Weak transcription	Primary B cells from cord blood	blood
46	chr10:94281200-94292600	Weak transcription	Hela-S3	cervix
47	chr10:94283400-94297400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:94285800-94295400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr10:94286200-94297600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr10:94286400-94298200	Strong transcription	Monocytes-CD14+_RO01746	blood

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