Variant report

Variant	rs7090996
Chromosome Location	chr10:52374289-52374290
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: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	chr10:52373141..52377774-chr10:52378271..52384648,13	K562	blood:
2	chr10:52369031..52370676-chr10:52373294..52376073,2	MCF-7	breast:
3	chr10:52340715..52342372-chr10:52372792..52375032,2	MCF-7	breast:
4	chr10:52361957..52364109-chr10:52372914..52375707,2	K562	blood:
5	chr10:52371729..52375098-chr10:52383274..52385073,4	MCF-7	breast:
6	chr10:52372893..52376676-chr10:52385065..52387133,3	K562	blood:
7	chr10:52321608..52322162-chr10:52374026..52374665,2	K562	blood:
8	chr10:52366580..52370875-chr10:52371309..52374318,4	K562	blood:
9	chr10:52321488..52322151-chr10:52374019..52374674,2	MCF-7	breast:
10	chr10:52371856..52377048-chr10:52377440..52385994,18	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10740762	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10763590	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10826242	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11006281	0.97[ASN][1000 genomes]
rs17497064	0.94[ASN][1000 genomes]
rs3001879	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3001883	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3001885	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011714	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4268459	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4935735	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4935736	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4935737	0.94[ASN][1000 genomes]
rs4935739	0.93[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6481442	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6481461	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7067552	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7073182	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7089882	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7094655	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7097359	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7903649	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7904101	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7908136	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7909486	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7918559	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7090996	FLJ31958	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr10:52364400-52374400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr10:52365400-52375000	Weak transcription	Fetal Brain Female	brain
4	chr10:52365400-52379400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr10:52365600-52377200	Weak transcription	Primary T cells from cord blood	blood
6	chr10:52365800-52378200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr10:52366000-52381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:52366600-52377800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:52367200-52377800	Weak transcription	Primary B cells from cord blood	blood
10	chr10:52367200-52379400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr10:52367400-52381400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:52367600-52378400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:52367600-52381400	Weak transcription	NHLF	lung
14	chr10:52367600-52381400	Weak transcription	Osteobl	bone
15	chr10:52368200-52375400	Enhancers	Pancreas	Pancrea
16	chr10:52369000-52378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr10:52369200-52375800	Enhancers	Fetal Heart	heart
18	chr10:52369400-52375400	Enhancers	Brain Anterior Caudate	brain
19	chr10:52369600-52374800	Enhancers	Brain Cingulate Gyrus	brain
20	chr10:52369600-52375400	Enhancers	Psoas Muscle	Psoas
21	chr10:52369600-52375400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr10:52369600-52375800	Enhancers	Brain Angular Gyrus	brain
23	chr10:52369600-52375800	Enhancers	Brain Hippocampus Middle	brain
24	chr10:52369800-52374400	Enhancers	Brain Substantia Nigra	brain
25	chr10:52369800-52376200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:52370200-52378400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:52370600-52374400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:52370800-52378400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:52371000-52381200	Weak transcription	Fetal Stomach	stomach
30	chr10:52371200-52374400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr10:52371200-52378200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr10:52371200-52381600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr10:52371400-52375400	Enhancers	Liver	Liver
34	chr10:52371600-52374800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr10:52371600-52374800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr10:52371600-52375000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr10:52371800-52375600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr10:52371800-52378400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:52372000-52374400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr10:52372000-52374600	Enhancers	GM12878-XiMat	blood
41	chr10:52372000-52375200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr10:52372200-52375200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr10:52372400-52374600	Enhancers	Esophagus	oesophagus
44	chr10:52372400-52374800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:52372400-52374800	Enhancers	Lung	lung
46	chr10:52372400-52375200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr10:52372600-52374800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr10:52372600-52374800	Enhancers	Right Atrium	heart
49	chr10:52372600-52374800	Enhancers	HepG2	liver
50	chr10:52372600-52381600	Weak transcription	Aorta	Aorta

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