Variant report

Variant	rs3787577
Chromosome Location	chr21:17168379-17168380
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	chr21:17163468..17165949-chr21:17167701..17169512,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10482875	0.83[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes]
rs10482876	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11910884	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1543299	0.91[CEU][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17241409	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17241416	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17241423	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17241430	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17241444	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17241460	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17241481	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17275511	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17307120	0.83[CEU][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs17307170	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17307176	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17307190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17307197	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17307204	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2026853	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2205585	0.95[EUR][1000 genomes]
rs2205588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2205589	0.89[EUR][1000 genomes]
rs2223176	0.95[EUR][1000 genomes]
rs2242676	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242677	0.93[ASN][1000 genomes]
rs2242680	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2242681	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2245574	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2274797	1.00[MEX][hapmap]
rs2404000	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2404001	0.83[CEU][hapmap]
rs2823455	0.91[CEU][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs2823462	0.83[CEU][hapmap]
rs2823463	0.83[CEU][hapmap]
rs2823471	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2823472	1.00[CEU][hapmap]
rs2823478	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2823489	1.00[CEU][hapmap]
rs2823491	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2823493	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2823495	0.95[EUR][1000 genomes]
rs2823496	0.95[EUR][1000 genomes]
rs2823497	0.92[EUR][1000 genomes]
rs2823498	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2823499	1.00[CEU][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs2823500	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2823504	0.91[CEU][hapmap]
rs2823505	0.94[EUR][1000 genomes]
rs2823513	0.81[EUR][1000 genomes]
rs55806628	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56299770	0.88[ASN][1000 genomes]
rs56333224	0.90[AMR][1000 genomes]
rs56410772	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56666611	0.82[EUR][1000 genomes]
rs57733106	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57737796	0.82[ASN][1000 genomes]
rs59084861	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59420372	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60191002	0.88[ASN][1000 genomes]
rs60360638	0.88[ASN][1000 genomes]
rs60529604	0.90[AMR][1000 genomes]
rs6517609	1.00[CEU][hapmap]
rs6517613	1.00[CEU][hapmap]
rs6517648	1.00[CEU][hapmap]
rs6517652	1.00[CEU][hapmap]
rs6517675	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7277807	0.83[CEU][hapmap]
rs7278428	0.83[CEU][hapmap]
rs7278727	0.91[EUR][1000 genomes]
rs7281511	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7282314	0.82[AMR][1000 genomes]
rs7283707	1.00[CEU][hapmap]
rs7283764	0.83[CEU][hapmap];0.88[ASN][1000 genomes]
rs73181987	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73346766	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73346769	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73357260	0.82[EUR][1000 genomes]
rs8127158	1.00[CEU][hapmap]
rs8128073	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8128766	0.94[EUR][1000 genomes]
rs8133079	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8134327	0.91[CEU][hapmap]
rs9974210	0.94[EUR][1000 genomes]
rs9976815	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977000	0.92[EUR][1000 genomes]
rs9977069	0.81[EUR][1000 genomes]
rs9981766	0.95[EUR][1000 genomes]
rs9983248	0.94[EUR][1000 genomes]
rs9983385	0.94[EUR][1000 genomes]
rs9983542	0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs9983858	0.94[EUR][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	nsv834050	chr21:17146090-17348951	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1063035	chr21:17154222-17224344	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3787577	MXRA7	trans	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17151800-17191000	Weak transcription	NH-A	brain
2	chr21:17155000-17171000	Weak transcription	Dnd41	blood
3	chr21:17155000-17179800	Weak transcription	Spleen	Spleen
4	chr21:17155000-17187400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr21:17155000-17188600	Weak transcription	HepG2	liver
6	chr21:17155200-17168600	Weak transcription	K562	blood
7	chr21:17155200-17169800	Weak transcription	Liver	Liver
8	chr21:17155200-17169800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr21:17155200-17177000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr21:17155200-17177000	Weak transcription	Brain Anterior Caudate	brain
11	chr21:17155200-17177000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr21:17155200-17177000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr21:17155200-17179200	Weak transcription	Fetal Intestine Large	intestine
14	chr21:17155200-17179200	Weak transcription	Left Ventricle	heart
15	chr21:17155200-17181200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr21:17155200-17181400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr21:17155200-17181400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr21:17155200-17182200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr21:17155200-17183200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr21:17155200-17183200	Weak transcription	Placenta	Placenta
21	chr21:17155200-17184600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr21:17155200-17186200	Weak transcription	Fetal Thymus	thymus
23	chr21:17155200-17187200	Weak transcription	Thymus	Thymus
24	chr21:17155200-17187400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr21:17155200-17187800	Weak transcription	Fetal Kidney	kidney
26	chr21:17155200-17189800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr21:17155200-17197600	Weak transcription	Fetal Heart	heart
28	chr21:17155200-17199200	Weak transcription	Right Ventricle	heart
29	chr21:17155200-17203800	Weak transcription	Colon Smooth Muscle	Colon
30	chr21:17155200-17209800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr21:17155200-17252800	Weak transcription	Fetal Brain Male	brain
32	chr21:17155400-17169000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr21:17155600-17176800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr21:17155600-17179200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr21:17155600-17182000	Weak transcription	Fetal Lung	lung
36	chr21:17155800-17169400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr21:17155800-17176800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr21:17155800-17177200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr21:17155800-17185400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr21:17155800-17186200	Weak transcription	Fetal Muscle Leg	muscle
41	chr21:17155800-17187200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr21:17156000-17176200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr21:17157000-17178400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr21:17161400-17168800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr21:17161400-17187200	Weak transcription	Aorta	Aorta
46	chr21:17161600-17172600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr21:17161600-17187400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr21:17162000-17177200	Weak transcription	NHDF-Ad	bronchial
49	chr21:17162000-17182000	Weak transcription	Osteobl	bone
50	chr21:17162400-17171400	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links