Variant report

Variant	rs4928230
Chromosome Location	chr3:99661963-99661964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99638580..99640218-chr3:99660275..99662821,2	K562	blood:
2	chr3:99657995..99660872-chr3:99661118..99663012,2	MCF-7	breast:
3	chr3:99658541..99660267-chr3:99661870..99663400,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10936003	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11711935	0.81[LWK][hapmap];0.90[MKK][hapmap]
rs11719468	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12488245	0.81[CEU][hapmap]
rs1287284	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs13059754	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap]
rs1384062	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1387647	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs1610509	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs16841874	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs1718235	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577503	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.84[ASN][1000 genomes]
rs4928150	0.84[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs4928151	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs4928153	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4928237	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs58704213	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440967	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs6788750	0.86[LWK][hapmap];0.94[MKK][hapmap]
rs6802817	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs6806323	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs704571	0.94[JPT][hapmap]
rs704572	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs704574	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs7613864	0.84[ASN][1000 genomes]
rs7649349	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs7650727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs766778	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs792831	0.94[JPT][hapmap]
rs792833	0.86[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs792835	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs792836	0.94[JPT][hapmap]
rs792837	0.94[JPT][hapmap]
rs793437	0.82[ASN][1000 genomes]
rs793439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793443	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs793446	0.84[CEU][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs793450	0.88[LWK][hapmap];0.88[MKK][hapmap]
rs793456	0.80[ASN][1000 genomes]
rs793464	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.84[ASN][1000 genomes]
rs793469	0.88[LWK][hapmap];0.90[MKK][hapmap]
rs793475	0.83[CEU][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs793476	0.85[ASN][1000 genomes]
rs793482	0.82[YRI][hapmap]
rs793483	0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs793485	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs793497	0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs793502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs796976	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs813218	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs902159	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs923472	0.84[CEU][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4928230	OR5H6	cis	cerebellum	SCAN
rs4928230	C3orf26	cis	multi-tissue	Pritchard
rs4928230	SENP7	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99644800-99663200	Weak transcription	Esophagus	oesophagus
2	chr3:99648800-99663200	Weak transcription	Gastric	stomach
3	chr3:99648800-99664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:99649600-99662800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:99650400-99663000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:99650400-99667400	Weak transcription	A549	lung
7	chr3:99650600-99662800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:99650600-99663200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:99654000-99663000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:99654600-99664000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:99654800-99663000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:99654800-99663000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:99654800-99663000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:99654800-99663200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:99655200-99663000	Weak transcription	Brain Anterior Caudate	brain
16	chr3:99656600-99662800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:99657200-99662600	Weak transcription	Brain Angular Gyrus	brain
18	chr3:99657400-99663000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:99657400-99663200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:99657600-99662600	Weak transcription	Brain Germinal Matrix	brain
21	chr3:99657600-99663000	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
23	chr3:99657800-99662800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:99657800-99662800	Weak transcription	Fetal Heart	heart
25	chr3:99657800-99662800	Weak transcription	HSMMtube	muscle
26	chr3:99657800-99662800	Weak transcription	NHDF-Ad	bronchial
27	chr3:99657800-99663000	Weak transcription	Fetal Brain Male	brain
28	chr3:99657800-99663000	Weak transcription	NHEK	skin
29	chr3:99657800-99663400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:99657800-99663400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:99657800-99664200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:99657800-99664200	Weak transcription	Fetal Brain Female	brain
33	chr3:99658000-99663000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:99658200-99662600	Weak transcription	Left Ventricle	heart
35	chr3:99658200-99662800	Weak transcription	NH-A	brain
36	chr3:99658200-99662800	Weak transcription	Osteobl	bone
37	chr3:99658200-99663000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:99658200-99663000	Weak transcription	NHLF	lung
39	chr3:99658200-99663400	Weak transcription	Right Ventricle	heart
40	chr3:99658400-99662600	Weak transcription	HSMM	muscle
41	chr3:99658400-99662800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:99658400-99663200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:99658400-99663200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:99658400-99664400	Weak transcription	Small Intestine	intestine
45	chr3:99658600-99663000	Weak transcription	Fetal Intestine Large	intestine
46	chr3:99658600-99663000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:99658800-99663600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:99659000-99662600	Weak transcription	Fetal Lung	lung
49	chr3:99659200-99663600	Weak transcription	Fetal Intestine Small	intestine
50	chr3:99659400-99662800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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