Variant report

Variant	rs902906
Chromosome Location	chr10:25351196-25351197
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:25350138..25352241-chr10:25355108..25357944,2	MCF-7	breast:
2	chr10:25344528..25346562-chr10:25350767..25353027,3	K562	blood:
3	chr10:25343578..25346366-chr10:25349000..25351556,3	MCF-7	breast:
4	chr10:25303827..25307133-chr10:25349437..25354097,8	K562	blood:
5	chr10:25334592..25336921-chr10:25350299..25353033,2	K562	blood:
6	chr10:25349510..25351855-chr10:25352161..25354821,2	MCF-7	breast:
7	chr10:25303827..25307969-chr10:25351029..25354599,5	K562	blood:
8	chr10:25307575..25310244-chr10:25349571..25352250,2	MCF-7	breast:
9	chr10:25344134..25348116-chr10:25349607..25352644,3	MCF-7	breast:
10	chr10:25304955..25307281-chr10:25348708..25354586,7	MCF-7	breast:
11	chr10:25239858..25243208-chr10:25347592..25352504,4	K562	blood:
12	chr10:25350226..25351753-chr10:25385209..25386887,2	K562	blood:
13	chr10:25306123..25307821-chr10:25350955..25353147,2	MCF-7	breast:
14	chr10:25239858..25242854-chr10:25350195..25352504,2	K562	blood:
15	chr10:25345062..25348953-chr10:25349936..25353027,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000151023	Chromatin interaction
ENSG00000099256	Chromatin interaction
ENSG00000273107	Chromatin interaction
ENSG00000185875	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10508685	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10508686	0.87[CEU][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs10828745	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10828747	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10828750	0.97[ASN][1000 genomes]
rs10828751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10828752	0.93[ASN][1000 genomes]
rs10828754	0.84[ASN][1000 genomes]
rs10828755	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11014360	0.87[EUR][1000 genomes]
rs11014361	0.89[EUR][1000 genomes]
rs11014362	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11014365	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11014367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11014368	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11014375	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014379	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11014389	0.82[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1124017	0.81[EUR][1000 genomes]
rs12219239	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12241661	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12243641	0.82[ASN][1000 genomes]
rs12249889	0.93[GIH][hapmap]
rs12251969	0.82[YRI][hapmap]
rs12256642	0.93[GIH][hapmap]
rs12764623	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12773782	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12776058	0.86[EUR][1000 genomes]
rs12784769	0.80[CEU][hapmap]
rs1352984	0.88[EUR][1000 genomes]
rs1352985	0.89[EUR][1000 genomes]
rs1492606	0.82[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1492607	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1492608	0.93[GIH][hapmap]
rs1546097	0.84[CEU][hapmap];0.95[GIH][hapmap]
rs1552770	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552771	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1907790	0.82[ASN][1000 genomes]
rs1907791	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1963584	0.89[ASN][1000 genomes]
rs2087781	0.91[JPT][hapmap]
rs2131275	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2220707	0.89[EUR][1000 genomes]
rs2291583	0.93[GIH][hapmap]
rs2307047	0.93[GIH][hapmap];0.80[LWK][hapmap]
rs2367507	0.89[ASN][1000 genomes]
rs4237369	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4508094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4747511	0.89[EUR][1000 genomes]
rs4748996	0.93[GIH][hapmap]
rs4748999	0.88[EUR][1000 genomes]
rs4749000	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4749001	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4749004	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4749005	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6482468	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7896122	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7898431	0.81[ASN][1000 genomes]
rs7911863	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs902904	0.93[GIH][hapmap]
rs923757	0.92[ASN][1000 genomes]
rs923758	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550224	chr10:25335854-25385858	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1036683	chr10:25337592-25398119	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv894969	chr10:25345720-25395579	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs902906	ENKUR	cis	parietal	SCAN
rs902906	THNSL1	cis	parietal	SCAN
rs902906	THNSL1	cis	cerebellum	SCAN
rs902906	PIP4K2A	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25348200-25351200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:25348200-25351600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr10:25348200-25352200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:25348400-25351200	Enhancers	HUVEC	blood vessel
5	chr10:25348400-25351600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:25348400-25352200	Enhancers	Stomach Mucosa	stomach
7	chr10:25348400-25352800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:25348800-25352000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:25349000-25351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:25349200-25351200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr10:25349200-25351400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:25349200-25351400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:25349400-25351200	Weak transcription	NHDF-Ad	bronchial
14	chr10:25349800-25351200	Weak transcription	Placenta	Placenta
15	chr10:25350400-25351600	Flanking Active TSS	Fetal Intestine Small	intestine
16	chr10:25350400-25351800	Flanking Active TSS	K562	blood
17	chr10:25350600-25351200	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr10:25350600-25351200	Enhancers	HSMM	muscle
19	chr10:25350600-25351400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr10:25350600-25351400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr10:25350600-25351800	Enhancers	Pancreas	Pancrea
22	chr10:25350600-25351800	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr10:25350600-25351800	Flanking Active TSS	A549	lung
24	chr10:25350600-25351800	Flanking Active TSS	Hela-S3	cervix
25	chr10:25350600-25352000	Enhancers	Lung	lung
26	chr10:25350800-25351200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr10:25350800-25351200	Flanking Active TSS	Liver	Liver
28	chr10:25350800-25351200	Weak transcription	Gastric	stomach
29	chr10:25350800-25351200	Enhancers	HSMMtube	muscle
30	chr10:25350800-25351400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr10:25350800-25351600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr10:25350800-25351600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr10:25350800-25351600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:25350800-25351800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:25350800-25351800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr10:25350800-25351800	Flanking Active TSS	HepG2	liver
37	chr10:25350800-25351800	Flanking Active TSS	NH-A	brain
38	chr10:25351000-25351200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:25351000-25351200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr10:25351000-25351200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr10:25351000-25351400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr10:25351000-25351400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:25351000-25351400	Flanking Active TSS	Aorta	Aorta
44	chr10:25351000-25351400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr10:25351000-25351400	Flanking Active TSS	HMEC	breast
46	chr10:25351000-25351400	Flanking Active TSS	NHEK	skin
47	chr10:25351000-25351600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:25351000-25351600	Enhancers	Fetal Lung	lung
49	chr10:25351000-25351800	Active TSS	Colonic Mucosa	Colon
50	chr10:25351000-25351800	Flanking Active TSS	Osteobl	bone

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