Variant report

Variant	rs6963753
Chromosome Location	chr7:27902404-27902405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10951186	1.00[CEU][hapmap]
rs12154776	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12531244	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12531907	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12537135	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12700847	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12700848	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13224500	0.94[EUR][1000 genomes]
rs13237769	0.94[EUR][1000 genomes]
rs13247831	0.80[EUR][1000 genomes]
rs1544413	0.82[EUR][1000 genomes]
rs1544414	0.82[EUR][1000 genomes]
rs17155954	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17613082	0.83[EUR][1000 genomes]
rs17613350	0.83[EUR][1000 genomes]
rs34015232	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34594641	0.83[EUR][1000 genomes]
rs35801744	0.86[EUR][1000 genomes]
rs35971552	0.99[EUR][1000 genomes]
rs36057260	0.83[EUR][1000 genomes]
rs4455744	0.90[EUR][1000 genomes]
rs57088391	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71539544	0.80[EUR][1000 genomes]
rs739898	0.94[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1018550	chr7:27844038-27925645	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6963753	HIBADH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27875200-27913000	Weak transcription	Right Atrium	heart
2	chr7:27876200-27913000	Weak transcription	Fetal Heart	heart
3	chr7:27880600-27903000	Weak transcription	Lung	lung
4	chr7:27880600-27913600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:27880800-27913200	Weak transcription	Aorta	Aorta
6	chr7:27881000-27905600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr7:27882800-27912000	Weak transcription	Brain Anterior Caudate	brain
8	chr7:27883600-27903000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:27883800-27903000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:27889200-27912000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:27893200-27909000	Weak transcription	Right Ventricle	heart
12	chr7:27894400-27903200	Weak transcription	HMEC	breast
13	chr7:27894800-27903200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr7:27896000-27903400	Weak transcription	Fetal Stomach	stomach
15	chr7:27896000-27908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:27896200-27913600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:27896600-27907200	Weak transcription	Primary T cells from cord blood	blood
18	chr7:27897200-27902600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:27897200-27903000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:27897200-27903200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:27897200-27903400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:27897200-27906400	Weak transcription	Spleen	Spleen
23	chr7:27897200-27907400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:27897200-27909000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:27897200-27912000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:27897200-27915200	Weak transcription	Gastric	stomach
27	chr7:27898400-27907200	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:27899200-27903200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:27899200-27903600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:27899400-27912600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:27900600-27910200	Weak transcription	Pancreas	Pancrea
32	chr7:27900600-27911400	Weak transcription	Adipose Nuclei	Adipose
33	chr7:27900800-27902600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr7:27900800-27903000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr7:27901000-27908000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr7:27901200-27913400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr7:27901400-27908000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr7:27901400-27913400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:27901400-27913800	Weak transcription	NHLF	lung
40	chr7:27901600-27905800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr7:27901600-27912200	Strong transcription	Primary B cells from cord blood	blood
42	chr7:27901800-27909600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr7:27902000-27904200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:27902200-27911600	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links