Variant report

Variant	rs6684594
Chromosome Location	chr1:171774758-171774759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10798636	0.84[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10798667	0.94[ASN][1000 genomes]
rs10913644	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11587288	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11589823	0.81[AFR][1000 genomes]
rs11803889	0.89[YRI][hapmap]
rs12034454	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039034	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12566700	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs16843385	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232812	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232816	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232818	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232826	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294717	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753538	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56178029	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57476157	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59302445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60502293	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60956160	0.88[EUR][1000 genomes]
rs6425423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425438	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs6425439	0.93[ASN][1000 genomes]
rs6690544	0.83[ASW][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs6691222	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6695502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6700184	0.82[YRI][hapmap]
rs72703115	0.94[ASN][1000 genomes]
rs7541192	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543608	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556602	0.81[YRI][hapmap]
rs7860	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909958	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs941942	0.84[CEU][hapmap];0.87[EUR][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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6684594	MAEL	cis	parietal	SCAN
rs6684594	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs6684594	DNM3	cis	cerebellum	SCAN
rs6684594	VAMP4	cis	parietal	SCAN
rs6684594	ILDR2	cis	cerebellum	SCAN
rs6684594	METTL13	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171766000-171774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:171766200-171775400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:171766200-171777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:171766400-171777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:171766600-171774800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:171766600-171774800	Weak transcription	Placenta	Placenta
7	chr1:171766600-171774800	Weak transcription	HepG2	liver
8	chr1:171767000-171774800	Weak transcription	Osteobl	bone
9	chr1:171767000-171777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:171767000-171778600	Weak transcription	NHEK	skin
11	chr1:171767200-171774800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:171767200-171774800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:171767200-171777600	Weak transcription	HMEC	breast
14	chr1:171767400-171774800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:171767400-171774800	Weak transcription	Psoas Muscle	Psoas
16	chr1:171767400-171775000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:171767400-171777200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:171767600-171774800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:171767600-171774800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:171767600-171775000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:171767800-171774800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:171767800-171774800	Weak transcription	Aorta	Aorta
23	chr1:171767800-171778800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:171767800-171781800	Weak transcription	Thymus	Thymus
25	chr1:171768000-171774800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:171768000-171776600	Weak transcription	Esophagus	oesophagus
27	chr1:171768000-171778600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:171768200-171774800	Weak transcription	Spleen	Spleen
29	chr1:171768200-171774800	Weak transcription	HSMM	muscle
30	chr1:171768400-171775000	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:171768400-171785600	Weak transcription	Gastric	stomach
32	chr1:171769800-171775000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:171770200-171774800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:171770200-171794600	Weak transcription	Primary T cells from cord blood	blood
35	chr1:171770600-171784800	Weak transcription	Primary B cells from cord blood	blood
36	chr1:171771200-171774800	Weak transcription	Brain Anterior Caudate	brain
37	chr1:171771400-171776800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:171771800-171777200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:171772600-171774800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:171772600-171774800	Weak transcription	NHLF	lung
41	chr1:171772800-171775000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:171773000-171774800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:171773000-171774800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:171773000-171774800	Weak transcription	NHDF-Ad	bronchial
45	chr1:171773000-171796000	Weak transcription	Pancreas	Pancrea
46	chr1:171774200-171774800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:171774200-171774800	Enhancers	Brain Cingulate Gyrus	brain
48	chr1:171774200-171775000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:171774200-171775000	Enhancers	Lung	lung
50	chr1:171774200-171775000	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links