Variant report

Variant	rs3828928
Chromosome Location	chr6:110425340-110425341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:110416916..110418691-chr6:110423265..110425370,2	MCF-7	breast:
2	chr6:110423972..110426062-chr6:110431154..110433493,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12660108	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12662027	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12662099	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12662559	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12664024	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12664697	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12665152	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12665178	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665650	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1350943	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1350944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1381688	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1462491	0.83[ASN][1000 genomes]
rs2002631	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2361500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2885293	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806158	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41288574	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41288576	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56662730	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57771959	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58100980	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58965432	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59181827	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60105161	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61494781	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6904509	0.91[ASN][1000 genomes]
rs6918158	0.88[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs6922245	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6922536	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6926993	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6927464	0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6935544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6937364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6941101	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73765657	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73765660	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73765665	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7752069	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7770634	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7771649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7771909	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9374151	1.00[EUR][1000 genomes]
rs9374152	0.83[ASN][1000 genomes]
rs9374153	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9374154	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9374155	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9374157	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9386877	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9386878	0.80[ASN][1000 genomes]
rs9386879	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9400361	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9400362	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9487324	0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886535	chr6:110377006-110551463	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv2757188	chr6:110389926-110504680	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv2759462	chr6:110389926-110504680	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1792799	chr6:110411065-110566597	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110417200-110438600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:110418200-110436000	Weak transcription	Fetal Brain Male	brain
3	chr6:110418800-110429000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:110418800-110437200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:110419000-110426600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:110419000-110427400	Weak transcription	Fetal Lung	lung
7	chr6:110419000-110428000	Weak transcription	HSMM	muscle
8	chr6:110419000-110431800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:110419000-110449600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:110419000-110461800	Weak transcription	HSMMtube	muscle
11	chr6:110419200-110449600	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:110419400-110430800	Weak transcription	Osteobl	bone
13	chr6:110419800-110429800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr6:110419800-110436400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:110420000-110430000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:110420200-110427000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:110420400-110431200	Weak transcription	Fetal Heart	heart
18	chr6:110420600-110426400	Weak transcription	Left Ventricle	heart
19	chr6:110420600-110435200	Weak transcription	Brain Anterior Caudate	brain
20	chr6:110421200-110430200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:110421200-110433400	Weak transcription	K562	blood
22	chr6:110421400-110430000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:110421600-110425400	Strong transcription	Liver	Liver
24	chr6:110422400-110426200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:110422600-110425400	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:110422800-110428200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:110423000-110426400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:110423200-110427400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:110423200-110427400	Weak transcription	Gastric	stomach
30	chr6:110423200-110429600	Weak transcription	NH-A	brain
31	chr6:110423200-110440800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:110423200-110448400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr6:110423400-110425600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:110423400-110426200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:110423400-110426200	Weak transcription	NHLF	lung
36	chr6:110423400-110426600	Weak transcription	Pancreas	Pancrea
37	chr6:110423400-110427800	Weak transcription	HepG2	liver
38	chr6:110423400-110431400	Weak transcription	Fetal Thymus	thymus
39	chr6:110423400-110434000	Weak transcription	HMEC	breast
40	chr6:110423400-110437600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:110423400-110439000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:110423400-110445000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:110423400-110450000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:110423400-110459000	Weak transcription	Fetal Stomach	stomach
45	chr6:110423400-110459200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:110423400-110459200	Weak transcription	Aorta	Aorta
47	chr6:110423600-110427800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr6:110423800-110426000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:110423800-110426800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:110423800-110427000	Weak transcription	Primary B cells from cord blood	blood

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