Variant report

Variant	rs3798430
Chromosome Location	chr6:76603852-76603853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1045758	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10806047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10806051	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943277	0.88[ASN][1000 genomes]
rs10943278	0.88[ASN][1000 genomes]
rs10943279	0.88[ASN][1000 genomes]
rs10943287	1.00[ASN][1000 genomes]
rs10943294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153964	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192223	0.88[ASN][1000 genomes]
rs12196105	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203091	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203148	0.88[ASN][1000 genomes]
rs12203461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205818	0.88[ASN][1000 genomes]
rs12208368	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12210386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211167	1.00[ASN][1000 genomes]
rs12211173	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212171	0.88[ASN][1000 genomes]
rs12212604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12213795	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215965	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191097	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13193694	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196164	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204537	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205073	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211391	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216921	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220416	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17792773	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1923586	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2208798	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34636573	0.88[ASN][1000 genomes]
rs3778008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798437	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798441	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798455	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71561437	0.84[ASN][1000 genomes]
rs71561438	0.81[ASN][1000 genomes]
rs9341531	0.88[ASN][1000 genomes]
rs9341534	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9341535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9341540	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9343315	0.88[ASN][1000 genomes]
rs9343320	0.88[ASN][1000 genomes]
rs9343326	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9350596	0.88[ASN][1000 genomes]
rs9350602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352241	1.00[ASN][1000 genomes]
rs9352244	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352245	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9359135	0.88[ASN][1000 genomes]
rs9359144	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9359148	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360930	0.88[ASN][1000 genomes]
rs9360932	0.88[ASN][1000 genomes]
rs9360939	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9360942	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360946	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360947	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360948	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360952	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360956	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447540	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];1.00[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	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3798430	CD109	cis	parietal	SCAN
rs3798430	DPPA5	cis	cerebellum	SCAN
rs3798430	RIMS1	cis	cerebellum	SCAN
rs3798430	MYO6	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:76566200-76604600	Weak transcription	Right Ventricle	heart
3	chr6:76567000-76604400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:76567600-76604200	Weak transcription	NHLF	lung
5	chr6:76573000-76624000	Weak transcription	Placenta	Placenta
6	chr6:76573200-76604200	Weak transcription	Colonic Mucosa	Colon
7	chr6:76573600-76606200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:76573800-76607200	Weak transcription	Gastric	stomach
9	chr6:76573800-76608400	Weak transcription	Esophagus	oesophagus
10	chr6:76574400-76632600	Weak transcription	Spleen	Spleen
11	chr6:76576000-76604000	Weak transcription	Fetal Brain Female	brain
12	chr6:76577200-76624600	Weak transcription	Fetal Kidney	kidney
13	chr6:76583400-76606200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:76583800-76624600	Weak transcription	Pancreas	Pancrea
15	chr6:76584000-76605600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:76584200-76608400	Weak transcription	Aorta	Aorta
17	chr6:76584200-76629400	Weak transcription	Ovary	ovary
18	chr6:76584400-76623800	Weak transcription	Lung	lung
19	chr6:76584800-76615200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:76584800-76644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:76585000-76608200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:76585800-76608000	Weak transcription	NH-A	brain
23	chr6:76585800-76624000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:76585800-76624400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:76585800-76626800	Weak transcription	Left Ventricle	heart
26	chr6:76585800-76644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:76586000-76627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:76586200-76624400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:76586400-76607800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:76587600-76623800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:76592000-76606000	Weak transcription	Adipose Nuclei	Adipose
32	chr6:76592200-76605400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:76592600-76624400	Weak transcription	Osteobl	bone
34	chr6:76592800-76606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:76592800-76631800	Weak transcription	NHEK	skin
36	chr6:76593200-76606000	Weak transcription	HSMM	muscle
37	chr6:76593200-76606200	Weak transcription	NHDF-Ad	bronchial
38	chr6:76594400-76608400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:76594600-76632200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:76597200-76604000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:76597200-76608400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:76597200-76624600	Weak transcription	Brain Angular Gyrus	brain
43	chr6:76599200-76604200	Strong transcription	Fetal Intestine Large	intestine
44	chr6:76599800-76604400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:76600200-76604000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:76600200-76631800	Weak transcription	HMEC	breast
47	chr6:76600400-76624600	Weak transcription	Brain Substantia Nigra	brain
48	chr6:76600600-76608200	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:76601400-76611600	Weak transcription	Fetal Stomach	stomach
50	chr6:76601600-76604400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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