Variant report

Variant	rs8028785
Chromosome Location	chr15:43130646-43130647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10162939	0.90[JPT][hapmap]
rs10518779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518793	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1197550	0.90[JPT][hapmap]
rs1197551	0.90[JPT][hapmap]
rs12905385	0.86[ASW][hapmap]
rs12914570	0.90[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs12917018	0.85[MEX][hapmap]
rs16957020	0.85[MEX][hapmap]
rs16957168	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs16957277	0.90[JPT][hapmap]
rs2136899	1.00[JPT][hapmap]
rs2136900	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2175370	0.90[JPT][hapmap]
rs2305084	1.00[JPT][hapmap];0.92[MEX][hapmap]
rs2305085	0.82[YRI][hapmap]
rs2412748	0.89[EUR][1000 genomes]
rs28374998	0.82[EUR][1000 genomes]
rs28392857	0.83[ASN][1000 genomes]
rs28494835	0.82[EUR][1000 genomes]
rs28609797	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28613047	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28620320	0.88[EUR][1000 genomes]
rs28633493	0.84[EUR][1000 genomes]
rs28649962	0.83[ASN][1000 genomes]
rs28674880	0.83[ASN][1000 genomes]
rs28796057	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28810091	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28858165	0.83[ASN][1000 genomes]
rs28871732	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3742993	1.00[JPT][hapmap]
rs3759792	0.87[EUR][1000 genomes]
rs4924694	0.83[MEX][hapmap]
rs4924699	0.85[CEU][hapmap]
rs6493059	1.00[JPT][hapmap];0.92[MEX][hapmap]
rs66947001	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166705	0.82[EUR][1000 genomes]
rs7166775	0.86[CEU][hapmap]
rs7167392	0.87[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap]
rs7169009	0.85[MEX][hapmap]
rs7175582	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs7178248	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7181859	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7182141	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap]
rs7182515	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8024902	0.90[JPT][hapmap]
rs8031218	0.84[MEX][hapmap]
rs8036674	0.82[EUR][1000 genomes]
rs8037613	0.85[CEU][hapmap]
rs8039711	0.90[JPT][hapmap]
rs8039765	0.90[JPT][hapmap];0.84[MEX][hapmap]
rs9269	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs938047	0.90[JPT][hapmap]
rs9919994	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs9920061	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9920163	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs9920182	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9920202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8028785	CDAN1	cis	parietal	SCAN
rs8028785	MAP1A	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:43063400-43136200	Weak transcription	Psoas Muscle	Psoas
3	chr15:43064800-43150800	Weak transcription	HSMM	muscle
4	chr15:43067400-43147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:43075200-43143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:43075400-43135800	Weak transcription	HSMMtube	muscle
7	chr15:43075600-43150800	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:43075800-43134800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:43075800-43159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:43089800-43165200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:43091800-43135400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:43094400-43163800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:43094600-43150800	Weak transcription	Aorta	Aorta
14	chr15:43095000-43165000	Weak transcription	Spleen	Spleen
15	chr15:43095600-43136000	Weak transcription	Fetal Brain Female	brain
16	chr15:43095800-43130800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:43095800-43130800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:43095800-43139000	Weak transcription	Esophagus	oesophagus
19	chr15:43096000-43133800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:43096000-43135600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:43096000-43136000	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:43096200-43136000	Weak transcription	Lung	lung
23	chr15:43097200-43131200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:43103000-43131200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:43103000-43131200	Weak transcription	Dnd41	blood
26	chr15:43103000-43133400	Weak transcription	Brain Substantia Nigra	brain
27	chr15:43103000-43134600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:43103000-43136000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:43103000-43165400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:43103200-43138400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:43103400-43133800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:43103400-43136000	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:43103400-43173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:43103800-43131200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr15:43106000-43136000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:43106200-43142000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:43107400-43134400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:43108200-43136200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:43110800-43136000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:43112600-43138000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:43113400-43131000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:43114800-43172000	Weak transcription	Pancreas	Pancrea
43	chr15:43118200-43139200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:43118400-43144400	Weak transcription	Gastric	stomach
45	chr15:43119200-43131200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:43119200-43136000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:43119400-43130800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:43119600-43131200	Weak transcription	Brain Angular Gyrus	brain
49	chr15:43119600-43136200	Weak transcription	Fetal Lung	lung
50	chr15:43119600-43168200	Weak transcription	Stomach Smooth Muscle	stomach

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