Variant report

Variant	rs4666441
Chromosome Location	chr2:20813657-20813658
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20791915..20794590-chr2:20811997..20814487,2	MCF-7	breast:
2	chr2:20807940..20810895-chr2:20811294..20813861,2	K562	blood:
3	chr2:20812051..20815064-chr2:20816352..20817928,3	K562	blood:
4	chr2:20644675..20653597-chr2:20811663..20819940,20	MCF-7	breast:
5	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
6	chr2:20807683..20810867-chr2:20811760..20818347,7	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf43-4	chr2:20812057-20816027	NONHSAT069462

No data

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10495708	0.90[CEU][hapmap];0.93[ASN][1000 genomes]
rs13003661	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[TSI][hapmap]
rs13027694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17662465	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17662495	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17662614	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17662644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17663045	0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17719096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101445	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34216303	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405290	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35001606	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35264816	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35311387	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35404888	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35527388	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755927	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456661	1.00[CHB][hapmap]
rs56905664	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60541580	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531249	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]
rs67364128	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782402	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs870309	1.00[CHB][hapmap]
rs896736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306893	0.86[CHB][hapmap]

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	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	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
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4666441	WDR35	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20803200-20814000	Weak transcription	HSMM	muscle
2	chr2:20805200-20813800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:20805200-20814000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:20805200-20816000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:20808400-20814200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:20808400-20816400	Enhancers	Rectal Smooth Muscle	rectum
7	chr2:20808400-20816600	Enhancers	Colon Smooth Muscle	Colon
8	chr2:20808400-20816800	Enhancers	Adipose Nuclei	Adipose
9	chr2:20808400-20819600	Enhancers	Fetal Muscle Leg	muscle
10	chr2:20808600-20818600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:20808600-20819400	Enhancers	Brain Anterior Caudate	brain
12	chr2:20808600-20819800	Enhancers	Brain Substantia Nigra	brain
13	chr2:20809000-20817200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:20809400-20816200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr2:20809600-20813800	Weak transcription	NHEK	skin
16	chr2:20809600-20814000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:20809600-20814200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:20809600-20814200	Weak transcription	Brain Germinal Matrix	brain
19	chr2:20809600-20816600	Weak transcription	Fetal Thymus	thymus
20	chr2:20809600-20819200	Weak transcription	Primary T cells from cord blood	blood
21	chr2:20809800-20814000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:20809800-20815000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:20810000-20814400	Weak transcription	Small Intestine	intestine
24	chr2:20810400-20814400	Enhancers	HUVEC	blood vessel
25	chr2:20810600-20814000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:20810800-20819200	Weak transcription	Primary B cells from cord blood	blood
27	chr2:20810800-20819600	Enhancers	Brain Hippocampus Middle	brain
28	chr2:20811600-20813800	Weak transcription	K562	blood
29	chr2:20811600-20814200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:20811600-20814400	Weak transcription	Aorta	Aorta
31	chr2:20811600-20816200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:20811600-20816200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:20811600-20820200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:20811800-20813800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:20811800-20813800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:20811800-20813800	Weak transcription	NHLF	lung
37	chr2:20811800-20814000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:20811800-20814000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:20811800-20814000	Weak transcription	Pancreas	Pancrea
40	chr2:20811800-20814000	Enhancers	Stomach Smooth Muscle	stomach
41	chr2:20811800-20814000	Weak transcription	NH-A	brain
42	chr2:20811800-20814000	Weak transcription	NHDF-Ad	bronchial
43	chr2:20811800-20814000	Weak transcription	Osteobl	bone
44	chr2:20811800-20814200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:20811800-20814600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:20811800-20815800	Weak transcription	Fetal Kidney	kidney
47	chr2:20811800-20816000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:20811800-20816400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:20811800-20817200	Enhancers	HepG2	liver
50	chr2:20812000-20813800	Weak transcription	Duodenum Mucosa	Duodenum

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