Variant report

Variant	rs10908614
Chromosome Location	chr1:158019262-158019263
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10796989	0.89[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10796990	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10796991	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10796992	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10796993	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10796994	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10908613	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264879	1.00[CEU][hapmap];0.91[GIH][hapmap]
rs11580742	1.00[CHD][hapmap]
rs11585913	1.00[CHD][hapmap]
rs12047033	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17419936	0.89[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap]
rs17419999	0.89[CEU][hapmap]
rs17453741	0.89[CEU][hapmap]
rs1925033	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4246542	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4971122	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6427417	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs6686246	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[AMR][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	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
2	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1005196	chr1:158015996-158065522	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10908614	VPS39	trans	parietal	SCAN
rs10908614	SPRR3	cis	cerebellum	SCAN
rs10908614	GATAD2B	cis	cerebellum	SCAN
rs10908614	DCST1	cis	cerebellum	SCAN
rs10908614	KIRREL	cis	cerebellum	SCAN
rs10908614	ASH1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157997600-158047600	Weak transcription	Dnd41	blood
2	chr1:158001200-158047400	Weak transcription	Thymus	Thymus
3	chr1:158002400-158025400	Weak transcription	Fetal Brain Female	brain
4	chr1:158008000-158019600	Weak transcription	Colonic Mucosa	Colon
5	chr1:158008200-158023000	Weak transcription	A549	lung
6	chr1:158008200-158024600	Weak transcription	Placenta	Placenta
7	chr1:158009400-158024400	Weak transcription	Hela-S3	cervix
8	chr1:158009600-158022600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:158010000-158023000	Weak transcription	HSMM	muscle
10	chr1:158010200-158020600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:158012200-158019800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:158013000-158020600	Enhancers	Fetal Lung	lung
13	chr1:158013400-158020600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:158013600-158020600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:158013600-158025600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:158013800-158027000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:158015200-158025400	Weak transcription	Left Ventricle	heart
18	chr1:158015200-158036400	Weak transcription	Esophagus	oesophagus
19	chr1:158015400-158020000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:158015600-158022800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:158015600-158024200	Weak transcription	Fetal Intestine Large	intestine
22	chr1:158015600-158029800	Weak transcription	Gastric	stomach
23	chr1:158015800-158019600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:158016000-158019400	Weak transcription	Osteobl	bone
25	chr1:158016000-158021400	Weak transcription	Fetal Heart	heart
26	chr1:158016000-158025600	Weak transcription	Fetal Thymus	thymus
27	chr1:158016000-158025800	Weak transcription	Pancreas	Pancrea
28	chr1:158016200-158019400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:158016200-158019400	Weak transcription	NH-A	brain
30	chr1:158016200-158019400	Weak transcription	NHLF	lung
31	chr1:158016200-158020400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:158016200-158025600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:158016200-158025600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:158016200-158030200	Weak transcription	Fetal Intestine Small	intestine
35	chr1:158016400-158020200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:158016600-158019600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:158016600-158020400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:158016600-158022800	Weak transcription	NHDF-Ad	bronchial
39	chr1:158016600-158025000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:158016600-158028400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:158016800-158019400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:158016800-158019800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:158016800-158024400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:158016800-158024400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:158016800-158024800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:158016800-158028000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:158016800-158028600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:158016800-158029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:158017000-158019800	Weak transcription	NHEK	skin
50	chr1:158017000-158020200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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