Variant report

Variant	rs1687949
Chromosome Location	chr1:94747353-94747354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94741320..94745215-chr1:94746019..94749869,4	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11165098	0.94[ASN][1000 genomes]
rs11165104	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165105	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165111	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11587699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12069420	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12084043	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12090310	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12090491	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12096115	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1330855	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17111360	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1756254	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2150269	0.99[ASN][1000 genomes]
rs2774923	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28613199	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35493159	0.99[ASN][1000 genomes]
rs3789688	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3814019	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3827751	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs58466782	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59960594	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs722296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525008	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528831	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7530160	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7538484	0.96[ASN][1000 genomes]
rs7540684	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548951	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1687949	WDR41	cis	Temporal Cortex	GTEx
rs1687949	BARHL2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94734200-94748600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:94738400-94750000	Weak transcription	Pancreas	Pancrea
3	chr1:94738400-94750000	Weak transcription	HMEC	breast
4	chr1:94738600-94750200	Weak transcription	Fetal Kidney	kidney
5	chr1:94738800-94750600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:94744400-94747600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:94744800-94747600	Enhancers	HSMM	muscle
8	chr1:94744800-94747800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:94744800-94747800	Enhancers	HUVEC	blood vessel
10	chr1:94745200-94747400	Weak transcription	Fetal Stomach	stomach
11	chr1:94745200-94750400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:94745800-94747600	Enhancers	Right Atrium	heart
13	chr1:94746000-94747400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:94746200-94747600	Enhancers	NH-A	brain
15	chr1:94746200-94747600	Enhancers	NHDF-Ad	bronchial
16	chr1:94746200-94747600	Enhancers	Osteobl	bone
17	chr1:94746200-94747800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:94746200-94748600	Enhancers	Fetal Heart	heart
19	chr1:94746600-94747400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:94746800-94747400	Enhancers	Fetal Lung	lung
21	chr1:94746800-94747400	Enhancers	Rectal Smooth Muscle	rectum
22	chr1:94746800-94747600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:94746800-94747600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:94746800-94747600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:94746800-94747600	Enhancers	Adipose Nuclei	Adipose
26	chr1:94746800-94747600	Enhancers	Stomach Smooth Muscle	stomach
27	chr1:94746800-94747600	Enhancers	HSMMtube	muscle
28	chr1:94746800-94747600	Enhancers	NHLF	lung
29	chr1:94746800-94748200	Enhancers	Left Ventricle	heart
30	chr1:94746800-94748600	Enhancers	HepG2	liver
31	chr1:94747000-94747600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:94747000-94747600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:94747000-94747600	Enhancers	Fetal Muscle Leg	muscle
34	chr1:94747000-94747600	Enhancers	Right Ventricle	heart
35	chr1:94747200-94750200	Weak transcription	Stomach Mucosa	stomach

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