Variant report

Variant	rs6531249
Chromosome Location	chr2:20827198-20827199
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20826217..20828028-chr2:20848423..20850444,2	K562	blood:
2	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
3	chr2:20826020..20829529-chr2:20830645..20833872,5	MCF-7	breast:
4	chr2:20647196..20649386-chr2:20825674..20827981,2	K562	blood:
5	chr2:20672997..20675403-chr2:20825825..20827538,2	MCF-7	breast:
6	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
7	chr2:20816763..20821100-chr2:20824834..20828532,5	K562	blood:
8	chr2:20826367..20828028-chr2:20848944..20850812,2	K562	blood:
9	chr2:20818868..20821100-chr2:20824834..20827973,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495708	0.90[CEU][hapmap];0.88[CHB][hapmap];0.96[ASN][1000 genomes]
rs13003661	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[TSI][hapmap]
rs13027694	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17662465	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17662495	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17662614	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17662644	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17663045	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17719096	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17719114	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17719159	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305459	0.82[EUR][1000 genomes]
rs34101445	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34216303	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34405290	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35001606	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35264816	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35311387	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35404888	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35527388	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35755927	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3732150	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3732158	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4456661	1.00[CHB][hapmap]
rs4666441	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56905664	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60541580	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67364128	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72782402	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744663	0.82[EUR][1000 genomes]
rs745687	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870309	0.88[CHB][hapmap];0.80[EUR][1000 genomes]
rs896736	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9306893	1.00[CHB][hapmap];0.81[EUR][1000 genomes]

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	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv527901	chr2:20818458-20876386	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
8	nsv999269	chr2:20824833-20869372	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6531249	WDR35	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20831800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20817400-20827200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:20817400-20831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:20817400-20835200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:20817600-20832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:20817800-20833800	Weak transcription	Fetal Thymus	thymus
10	chr2:20818200-20828600	Weak transcription	Fetal Kidney	kidney
11	chr2:20818200-20835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:20818200-20835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:20818400-20828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:20818400-20828800	Weak transcription	Fetal Brain Male	brain
15	chr2:20818400-20831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:20818800-20833600	Weak transcription	A549	lung
17	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:20819200-20827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:20819400-20834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:20819800-20834200	Weak transcription	Osteobl	bone
23	chr2:20820600-20827200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:20820600-20849400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:20820800-20849600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:20821400-20831800	Weak transcription	NHEK	skin
27	chr2:20822000-20832600	Weak transcription	Hela-S3	cervix
28	chr2:20822200-20828800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:20823000-20833600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:20823000-20833600	Weak transcription	HSMMtube	muscle
31	chr2:20823000-20842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:20823200-20831800	Weak transcription	HMEC	breast
33	chr2:20823400-20834200	Weak transcription	Small Intestine	intestine
34	chr2:20824000-20833600	Strong transcription	Fetal Intestine Small	intestine
35	chr2:20824200-20827200	Weak transcription	Fetal Heart	heart
36	chr2:20824400-20827200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:20824400-20827800	Enhancers	Left Ventricle	heart
38	chr2:20824400-20828800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:20824400-20829000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:20824600-20827800	Enhancers	Adipose Nuclei	Adipose
41	chr2:20824600-20828600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:20824600-20828800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:20824600-20828800	Weak transcription	Brain Germinal Matrix	brain
44	chr2:20824600-20828800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:20824600-20829000	Weak transcription	Liver	Liver
46	chr2:20824600-20829000	Weak transcription	Fetal Lung	lung
47	chr2:20824600-20829200	Weak transcription	Fetal Brain Female	brain
48	chr2:20824600-20833600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:20824600-20834000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:20824600-20834200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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