Variant report

Variant	rs6427417
Chromosome Location	chr1:158009334-158009335
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10796989	0.89[CEU][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap]
rs10796990	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs10796991	0.89[CEU][hapmap]
rs10796993	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs10908613	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs10908614	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs11264879	1.00[CEU][hapmap]
rs11580742	1.00[CHD][hapmap]
rs11585913	1.00[CHD][hapmap]
rs17419936	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs17419999	0.89[CEU][hapmap]
rs17453741	0.89[CEU][hapmap]
rs1925033	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs4971122	1.00[CEU][hapmap]
rs6686246	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6427417	S100A14	cis	parietal	SCAN
rs6427417	VPS39	trans	parietal	SCAN
rs6427417	C1orf92	cis	parietal	SCAN
rs6427417	ASH1L	cis	cerebellum	SCAN
rs6427417	GATAD2B	cis	cerebellum	SCAN
rs6427417	DCST1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157997600-158047600	Weak transcription	Dnd41	blood
2	chr1:157999000-158013000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:158001200-158011800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:158001200-158047400	Weak transcription	Thymus	Thymus
5	chr1:158002400-158025400	Weak transcription	Fetal Brain Female	brain
6	chr1:158004800-158009400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:158005000-158009400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:158005000-158009600	Enhancers	Ovary	ovary
9	chr1:158005000-158010000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:158005000-158010200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:158005400-158009600	Enhancers	Adipose Nuclei	Adipose
12	chr1:158005800-158009600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:158006200-158009400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:158006200-158009400	Weak transcription	Stomach Mucosa	stomach
15	chr1:158006200-158009600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:158006400-158009800	Enhancers	HMEC	breast
17	chr1:158006800-158009400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:158007000-158010000	Enhancers	HUVEC	blood vessel
19	chr1:158007200-158009400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:158007200-158009800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:158007200-158010000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:158007200-158010000	Enhancers	Fetal Lung	lung
23	chr1:158007400-158009400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:158007400-158009400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:158007400-158009400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:158007400-158009400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:158007400-158009600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:158007400-158009600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:158007400-158009600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:158007400-158009600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:158007400-158009600	Enhancers	NH-A	brain
32	chr1:158007400-158009800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:158007400-158010000	Enhancers	Colon Smooth Muscle	Colon
34	chr1:158007400-158010000	Enhancers	NHDF-Ad	bronchial
35	chr1:158007600-158009400	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr1:158007600-158009400	Enhancers	Left Ventricle	heart
37	chr1:158007600-158009400	Enhancers	Right Ventricle	heart
38	chr1:158007600-158009600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:158007800-158013000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:158008000-158009800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:158008000-158011800	Weak transcription	Fetal Intestine Small	intestine
42	chr1:158008000-158012200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:158008000-158014800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:158008000-158019600	Weak transcription	Colonic Mucosa	Colon
45	chr1:158008200-158009600	Enhancers	NHLF	lung
46	chr1:158008200-158011400	Weak transcription	Lung	lung
47	chr1:158008200-158013000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:158008200-158013000	Weak transcription	Right Atrium	heart
49	chr1:158008200-158015000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:158008200-158018400	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links