Variant report

Variant	rs17613350
Chromosome Location	chr7:27826415-27826416
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10951174	0.90[CEU][hapmap]
rs10951186	0.86[CEU][hapmap]
rs11520772	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12155171	0.81[EUR][1000 genomes]
rs12531244	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs12531907	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs12532737	0.83[EUR][1000 genomes]
rs12537135	0.83[EUR][1000 genomes]
rs12700847	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs12700848	0.81[CEU][hapmap]
rs13224500	0.85[EUR][1000 genomes]
rs13227574	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs13231645	0.94[CEU][hapmap]
rs13232561	0.95[CEU][hapmap]
rs13236065	0.82[EUR][1000 genomes]
rs13237769	0.86[EUR][1000 genomes]
rs13247831	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1544413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1544414	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17155954	0.85[CEU][hapmap]
rs17613082	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34594641	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35105727	0.82[EUR][1000 genomes]
rs35232956	0.82[EUR][1000 genomes]
rs35536764	0.80[EUR][1000 genomes]
rs35801744	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35971552	0.83[EUR][1000 genomes]
rs36057260	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36114463	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4391326	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4455744	0.85[EUR][1000 genomes]
rs4722725	0.84[CEU][hapmap]
rs57088391	0.84[EUR][1000 genomes]
rs6944455	0.80[EUR][1000 genomes]
rs6946448	0.81[CEU][hapmap]
rs6963753	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6968631	0.82[EUR][1000 genomes]
rs6969043	0.82[EUR][1000 genomes]
rs6969207	0.82[EUR][1000 genomes]
rs71539544	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17613350	HIBADH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27781000-27861800	Weak transcription	Aorta	Aorta
2	chr7:27784800-27834000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:27784800-27878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:27787800-27826600	Weak transcription	Small Intestine	intestine
5	chr7:27790600-27835000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:27790600-27857400	Weak transcription	Colonic Mucosa	Colon
7	chr7:27798600-27847800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:27798600-27874000	Weak transcription	Brain Angular Gyrus	brain
9	chr7:27801200-27851800	Weak transcription	Fetal Brain Male	brain
10	chr7:27801400-27831400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:27801400-27838400	Weak transcription	Fetal Brain Female	brain
12	chr7:27801600-27852800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:27805800-27832200	Weak transcription	Fetal Stomach	stomach
14	chr7:27805800-27857600	Weak transcription	Esophagus	oesophagus
15	chr7:27806000-27882600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:27806400-27878600	Weak transcription	Right Ventricle	heart
17	chr7:27806600-27827800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr7:27810400-27831600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:27810400-27831600	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:27810800-27831600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:27811200-27832200	Weak transcription	Ovary	ovary
22	chr7:27811200-27833600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:27811400-27831200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:27811600-27827600	Weak transcription	Fetal Lung	lung
25	chr7:27811800-27831400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:27811800-27835000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:27812000-27828000	Weak transcription	GM12878-XiMat	blood
28	chr7:27815400-27826600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr7:27815600-27832400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:27815600-27833200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:27815600-27874000	Weak transcription	Pancreas	Pancrea
32	chr7:27817400-27831800	Weak transcription	Brain Substantia Nigra	brain
33	chr7:27817400-27836200	Weak transcription	Psoas Muscle	Psoas
34	chr7:27818800-27834800	Weak transcription	Gastric	stomach
35	chr7:27819600-27831200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:27820400-27847400	Weak transcription	Fetal Heart	heart
37	chr7:27820800-27833200	Weak transcription	Brain Germinal Matrix	brain
38	chr7:27820800-27836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:27823000-27827800	Weak transcription	NHEK	skin
40	chr7:27823200-27826600	Weak transcription	Stomach Mucosa	stomach
41	chr7:27823400-27831600	Weak transcription	Brain Anterior Caudate	brain
42	chr7:27823800-27878000	Weak transcription	Spleen	Spleen
43	chr7:27824200-27843000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr7:27824200-27876800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr7:27824400-27828800	Strong transcription	Fetal Thymus	thymus
46	chr7:27824400-27833000	Weak transcription	A549	lung
47	chr7:27824600-27829200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr7:27824600-27830000	Strong transcription	Placenta	Placenta
49	chr7:27824600-27830000	Strong transcription	Dnd41	blood
50	chr7:27824600-27833400	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links