Variant report

Variant	rs1012049
Chromosome Location	chr6:128530307-128530308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128529927..128532522-chr6:128841893..128843396,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12200548	0.84[AFR][1000 genomes]
rs1339197	0.83[ASW][hapmap]
rs17055441	0.94[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs3813371	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3813372	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3813373	0.88[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4243494	0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4421217	0.88[ASN][1000 genomes]
rs4897252	0.88[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6933029	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6938118	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7753945	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7767531	0.91[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap]
rs9375550	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9375551	0.85[ASN][1000 genomes]
rs9375552	0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375553	0.82[CHB][hapmap]
rs9388618	0.83[ASN][1000 genomes]
rs9388619	0.88[ASN][1000 genomes]
rs9388621	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9388622	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9398865	0.82[CHB][hapmap]
rs9398866	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9402023	0.88[CHB][hapmap];0.84[JPT][hapmap]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv604646	chr6:128421762-128531651	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv604647	chr6:128421762-128547177	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv886653	chr6:128455539-128555805	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv886654	chr6:128471938-128555805	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1012049	HEY2	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
2	chr6:128492600-128567800	Weak transcription	Ovary	ovary
3	chr6:128503200-128541800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:128505800-128538800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:128505800-128552200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:128506000-128561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:128514000-128530600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:128516000-128530400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:128520400-128536800	Weak transcription	Fetal Intestine Large	intestine
10	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:128522000-128560800	Weak transcription	Primary T cells from cord blood	blood
12	chr6:128522600-128530400	Weak transcription	Liver	Liver
13	chr6:128523800-128530400	Weak transcription	Right Ventricle	heart
14	chr6:128523800-128538200	Weak transcription	Fetal Thymus	thymus
15	chr6:128523800-128540600	Weak transcription	Lung	lung
16	chr6:128523800-128543600	Weak transcription	Left Ventricle	heart
17	chr6:128525000-128535000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr6:128525200-128539000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:128526400-128531000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:128526600-128530400	Weak transcription	Primary B cells from cord blood	blood
21	chr6:128526800-128541200	Weak transcription	Adipose Nuclei	Adipose
22	chr6:128527000-128543600	Weak transcription	Fetal Intestine Small	intestine
23	chr6:128527600-128561000	Weak transcription	Esophagus	oesophagus
24	chr6:128527800-128531200	Enhancers	HSMM	muscle
25	chr6:128528000-128531200	Enhancers	HSMMtube	muscle
26	chr6:128528000-128531400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:128528000-128531600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:128528200-128532000	Enhancers	NHEK	skin
29	chr6:128528200-128532400	Enhancers	HUVEC	blood vessel
30	chr6:128528200-128532600	Weak transcription	Fetal Brain Female	brain
31	chr6:128528200-128558400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:128528400-128530800	Weak transcription	Right Atrium	heart
33	chr6:128528400-128531000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:128528400-128531000	Enhancers	HepG2	liver
35	chr6:128528400-128561000	Weak transcription	Fetal Brain Male	brain
36	chr6:128528600-128530600	Weak transcription	Pancreas	Pancrea
37	chr6:128529000-128530800	Enhancers	HMEC	breast
38	chr6:128529000-128531000	Enhancers	NHDF-Ad	bronchial
39	chr6:128529000-128531200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:128529000-128531400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:128529000-128532000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:128529000-128538000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:128529200-128530400	Enhancers	Hela-S3	cervix
44	chr6:128529200-128531400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:128529200-128531400	Enhancers	NHLF	lung
46	chr6:128529200-128532000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:128529400-128531000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:128529400-128538200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:128529400-128552600	Weak transcription	Small Intestine	intestine
50	chr6:128529600-128538200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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