Variant report

Variant	rs6686246
Chromosome Location	chr1:158009712-158009713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10796989	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10796990	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10796991	0.86[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10796992	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10796993	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.80[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10796994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10908613	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10908614	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[AMR][1000 genomes]
rs11264876	1.00[ASN][1000 genomes]
rs11264879	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[YRI][hapmap]
rs11580742	1.00[CHD][hapmap]
rs11585913	1.00[CHD][hapmap]
rs12047033	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16839654	1.00[ASN][1000 genomes]
rs16839658	1.00[ASN][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];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4246542	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4971122	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58860692	1.00[ASN][1000 genomes]
rs59961209	1.00[ASN][1000 genomes]
rs6427417	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
rs6686246	VPS39	trans	parietal	SCAN
rs6686246	ASH1L	cis	cerebellum	SCAN
rs6686246	DCST1	cis	cerebellum	SCAN
rs6686246	KIRREL	cis	cerebellum	SCAN
rs6686246	SPRR3	cis	cerebellum	SCAN
rs6686246	GATAD2B	cis	cerebellum	SCAN

Chromatin state (count:78 , 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	chr1:158005000-158010000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:158005000-158010200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:158006400-158009800	Enhancers	HMEC	breast
9	chr1:158007000-158010000	Enhancers	HUVEC	blood vessel
10	chr1:158007200-158009800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:158007200-158010000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:158007200-158010000	Enhancers	Fetal Lung	lung
13	chr1:158007400-158009800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:158007400-158010000	Enhancers	Colon Smooth Muscle	Colon
15	chr1:158007400-158010000	Enhancers	NHDF-Ad	bronchial
16	chr1:158007800-158013000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:158008000-158009800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:158008000-158011800	Weak transcription	Fetal Intestine Small	intestine
19	chr1:158008000-158012200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:158008000-158014800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:158008000-158019600	Weak transcription	Colonic Mucosa	Colon
22	chr1:158008200-158011400	Weak transcription	Lung	lung
23	chr1:158008200-158013000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:158008200-158013000	Weak transcription	Right Atrium	heart
25	chr1:158008200-158015000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:158008200-158018400	Weak transcription	Spleen	Spleen
27	chr1:158008200-158023000	Weak transcription	A549	lung
28	chr1:158008200-158024600	Weak transcription	Placenta	Placenta
29	chr1:158008600-158010000	Enhancers	HSMM	muscle
30	chr1:158008600-158012800	Weak transcription	Fetal Heart	heart
31	chr1:158008800-158010000	Enhancers	HSMMtube	muscle
32	chr1:158008800-158010000	Genic enhancers	NHEK	skin
33	chr1:158008800-158012800	Weak transcription	Aorta	Aorta
34	chr1:158008800-158013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:158008800-158015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:158009000-158010000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:158009000-158013000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:158009000-158013000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:158009200-158011400	Weak transcription	Fetal Stomach	stomach
40	chr1:158009200-158012400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:158009200-158013000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:158009200-158013000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:158009200-158013000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:158009200-158013000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:158009200-158013200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:158009200-158013600	Weak transcription	Fetal Kidney	kidney
47	chr1:158009400-158009800	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:158009400-158010000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:158009400-158010000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:158009400-158010200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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