Variant report

Variant	rs11950902
Chromosome Location	chr5:79997734-79997735
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79996950..79999268-chr5:80000178..80002674,2	K562	blood:
2	chr5:79996688..79998349-chr5:79998892..80001446,3	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10040849	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11951910	0.89[CEU][hapmap]
rs1346463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1346464	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1382539	1.00[JPT][hapmap]
rs1382540	1.00[JPT][hapmap]
rs1382543	1.00[JPT][hapmap]
rs1620258	1.00[ASN][1000 genomes]
rs1628627	1.00[JPT][hapmap]
rs1643651	1.00[ASN][1000 genomes]
rs1650648	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1650650	1.00[JPT][hapmap]
rs1650651	1.00[JPT][hapmap]
rs1650652	1.00[JPT][hapmap]
rs1650653	1.00[JPT][hapmap]
rs1650654	1.00[JPT][hapmap]
rs1650658	1.00[JPT][hapmap]
rs1650663	1.00[JPT][hapmap]
rs1650665	1.00[JPT][hapmap]
rs1650666	1.00[JPT][hapmap]
rs1650667	1.00[JPT][hapmap]
rs1650670	1.00[JPT][hapmap]
rs1650688	0.88[ASN][1000 genomes]
rs1650692	1.00[JPT][hapmap]
rs1650737	1.00[ASN][1000 genomes]
rs1650742	0.83[ASN][1000 genomes]
rs1650747	1.00[ASN][1000 genomes]
rs1650749	1.00[ASN][1000 genomes]
rs1650750	1.00[ASN][1000 genomes]
rs1677628	1.00[JPT][hapmap]
rs1677629	1.00[JPT][hapmap]
rs1677630	1.00[ASN][1000 genomes]
rs1677635	1.00[JPT][hapmap]
rs1677638	1.00[JPT][hapmap]
rs1677639	1.00[JPT][hapmap]
rs1677641	1.00[JPT][hapmap]
rs1677643	1.00[JPT][hapmap]
rs1677645	1.00[JPT][hapmap]
rs1677650	1.00[JPT][hapmap]
rs1677652	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1677653	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1677654	1.00[ASN][1000 genomes]
rs1677655	1.00[ASN][1000 genomes]
rs1677703	1.00[JPT][hapmap]
rs1677707	1.00[ASN][1000 genomes]
rs1677709	1.00[ASN][1000 genomes]
rs16878166	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1824837	1.00[JPT][hapmap]
rs1824838	1.00[JPT][hapmap]
rs1824839	1.00[JPT][hapmap]
rs245331	1.00[ASN][1000 genomes]
rs245332	1.00[ASN][1000 genomes]
rs2560425	1.00[ASN][1000 genomes]
rs2618369	1.00[ASN][1000 genomes]
rs26267	1.00[ASN][1000 genomes]
rs2897262	1.00[JPT][hapmap]
rs32959	1.00[ASN][1000 genomes]
rs6151614	1.00[JPT][hapmap]
rs6151615	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6151618	1.00[JPT][hapmap]
rs6151619	1.00[JPT][hapmap]
rs6151620	1.00[JPT][hapmap]
rs6151665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6151770	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151838	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73123307	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73123310	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125413	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73125416	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73127211	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs836795	1.00[ASN][1000 genomes]
rs836798	1.00[ASN][1000 genomes]
rs836799	1.00[ASN][1000 genomes]
rs836800	1.00[ASN][1000 genomes]
rs836801	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs836802	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs836804	1.00[ASN][1000 genomes]
rs836806	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs836808	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs836809	1.00[ASN][1000 genomes]
rs836810	1.00[ASN][1000 genomes]
rs836813	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs836816	1.00[ASN][1000 genomes]
rs844368	1.00[ASN][1000 genomes]
rs844369	1.00[ASN][1000 genomes]
rs857016	1.00[ASN][1000 genomes]
rs861372	1.00[ASN][1000 genomes]
rs863214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11950902	DHFR	cis	Adipose Subcutaneous	GTEx
rs11950902	DHFR	cis	Whole Blood	GTEx
rs11950902	ANKRD34B	cis	Whole Blood	GTEx
rs11950902	DHFR	cis	Heart Left Ventricle	GTEx
rs11950902	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs11950902	DHFR	cis	Muscle Skeletal	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
2	chr5:79956400-80015600	Weak transcription	Psoas Muscle	Psoas
3	chr5:79958200-79998000	Weak transcription	Fetal Brain Male	brain
4	chr5:79962800-80015600	Weak transcription	A549	lung
5	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
6	chr5:79964000-79998000	Weak transcription	Aorta	Aorta
7	chr5:79964400-79999200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:79964800-79998000	Weak transcription	Gastric	stomach
9	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:79965000-80021400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:79969400-80001200	Weak transcription	NHLF	lung
12	chr5:79969600-80010600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:79971600-79999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr5:79971600-80022200	Weak transcription	HMEC	breast
15	chr5:79971800-79999200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:79971800-80003400	Weak transcription	NHDF-Ad	bronchial
17	chr5:79971800-80015400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:79972400-79999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:79972400-80010400	Weak transcription	NHEK	skin
21	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:79972800-80001600	Weak transcription	HUVEC	blood vessel
23	chr5:79973200-80021600	Weak transcription	NH-A	brain
24	chr5:79973400-80008800	Weak transcription	Brain Anterior Caudate	brain
25	chr5:79974000-80003000	Weak transcription	Fetal Heart	heart
26	chr5:79974000-80021200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:79975000-79998000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:79975200-80022800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:79975600-80015200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:79975600-80022000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:79975800-80002800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:79975800-80004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:79975800-80007000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:79975800-80008800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:79975800-80009200	Weak transcription	Pancreas	Pancrea
36	chr5:79975800-80015600	Weak transcription	Brain Substantia Nigra	brain
37	chr5:79975800-80015800	Weak transcription	Fetal Brain Female	brain
38	chr5:79976000-79998000	Weak transcription	Ovary	ovary
39	chr5:79976000-79999200	Weak transcription	Osteobl	bone
40	chr5:79976000-80000000	Weak transcription	Thymus	Thymus
41	chr5:79976000-80010400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:79976200-79999200	Weak transcription	HSMM	muscle
43	chr5:79976200-79999200	Weak transcription	HSMMtube	muscle
44	chr5:79976600-80003200	Weak transcription	Left Ventricle	heart
45	chr5:79976800-79998000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr5:79977200-79999200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr5:79978000-79999800	Weak transcription	Hela-S3	cervix
48	chr5:79979000-79998200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:79979200-80013800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:79979400-79999200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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