Variant report

Variant	rs236301
Chromosome Location	chr1:94113981-94113982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1011903	0.87[CEU][hapmap];0.82[GIH][hapmap]
rs11164963	0.87[CEU][hapmap];0.82[GIH][hapmap]
rs12084853	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12092517	0.85[CEU][hapmap]
rs12568405	1.00[JPT][hapmap]
rs1292929	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567791	0.87[CEU][hapmap];0.91[GIH][hapmap]
rs1772781	1.00[JPT][hapmap]
rs236266	1.00[JPT][hapmap]
rs236273	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs236284	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236285	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236287	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236288	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236291	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236292	0.98[ASN][1000 genomes]
rs236295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236306	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs236307	1.00[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes]
rs236308	0.90[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs236311	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs236312	1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs236313	1.00[JPT][hapmap]
rs236343	0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs236344	0.93[MEX][hapmap];0.84[AMR][1000 genomes]
rs368888	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs3767979	0.89[JPT][hapmap]
rs3767991	1.00[JPT][hapmap]
rs399649	1.00[JPT][hapmap]
rs423493	0.89[ASW][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6541387	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6541389	0.87[CEU][hapmap];0.91[ASN][1000 genomes]
rs6656270	0.85[CEU][hapmap]
rs6657709	0.87[CEU][hapmap]
rs6660740	0.87[CEU][hapmap];0.82[GIH][hapmap]
rs6684568	0.87[ASN][1000 genomes]
rs6701871	0.87[ASN][1000 genomes]
rs6702036	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6704479	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7519952	0.90[ASN][1000 genomes]
rs798213	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs798217	0.80[AMR][1000 genomes]
rs955470	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236301	F3	cis	cerebellum	SCAN
rs236301	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94088600-94118800	Weak transcription	Gastric	stomach
2	chr1:94091800-94117400	Weak transcription	Fetal Lung	lung
3	chr1:94094200-94120400	Weak transcription	Psoas Muscle	Psoas
4	chr1:94095600-94125400	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:94100000-94135800	Weak transcription	Fetal Stomach	stomach
6	chr1:94101600-94128800	Weak transcription	Right Ventricle	heart
7	chr1:94102000-94117200	Weak transcription	Lung	lung
8	chr1:94102000-94119800	Weak transcription	HSMMtube	muscle
9	chr1:94102000-94125400	Weak transcription	Fetal Kidney	kidney
10	chr1:94102000-94125600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:94102600-94114200	Weak transcription	Brain Substantia Nigra	brain
12	chr1:94102600-94119200	Weak transcription	Fetal Intestine Small	intestine
13	chr1:94102800-94119000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:94103000-94121800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:94103800-94135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:94104800-94117600	Weak transcription	HepG2	liver
17	chr1:94105000-94118200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:94105800-94117200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:94106400-94126000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:94106600-94114400	Strong transcription	HMEC	breast
21	chr1:94106800-94115200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:94106800-94118800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:94107000-94114400	Weak transcription	Left Ventricle	heart
24	chr1:94107200-94125600	Weak transcription	Aorta	Aorta
25	chr1:94107600-94114400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:94107600-94119200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:94107800-94120000	Weak transcription	Primary B cells from cord blood	blood
28	chr1:94108200-94114400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:94108200-94116600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:94108200-94118800	Weak transcription	NHDF-Ad	bronchial
31	chr1:94108200-94119400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:94108400-94114400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:94108400-94116200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:94108400-94116600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:94108400-94116600	Weak transcription	Osteobl	bone
36	chr1:94108400-94119000	Weak transcription	Adipose Nuclei	Adipose
37	chr1:94108400-94119200	Weak transcription	NHLF	lung
38	chr1:94108600-94114400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:94108600-94116400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:94108600-94116600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:94108600-94116600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:94108600-94117200	Weak transcription	Ovary	ovary
43	chr1:94108600-94122200	Weak transcription	HUVEC	blood vessel
44	chr1:94108600-94130400	Weak transcription	Esophagus	oesophagus
45	chr1:94108800-94114200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:94109000-94114400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:94110000-94119200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:94110200-94124400	Strong transcription	NHEK	skin
49	chr1:94110800-94114200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:94110800-94114200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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