Variant report

Variant	rs6662572
Chromosome Location	chr1:46146812-46146813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46145159..46149655-chr1:46150963..46155406,6	MCF-7	breast:
2	chr1:46049723..46052330-chr1:46146069..46149736,3	K562	blood:
3	chr1:46117400..46120287-chr1:46145313..46147738,2	K562	blood:
4	chr1:46049723..46052750-chr1:46146069..46149736,4	K562	blood:
5	chr1:46116859..46119732-chr1:46144618..46147111,2	K562	blood:

Variant related genes	Relation type
ENSG00000132780	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000234329	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1053941	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10749859	1.00[CHB][hapmap]
rs10789477	1.00[CHB][hapmap]
rs10890356	1.00[CHB][hapmap]
rs11211206	1.00[CHB][hapmap]
rs11211211	1.00[CHB][hapmap]
rs11579176	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs11582058	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11585275	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11587918	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11587982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590549	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12042481	1.00[ASW][hapmap]
rs2065708	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs28412451	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28433203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484896	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584711	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014232	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41310432	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4423055	1.00[CHB][hapmap]
rs4434876	1.00[CHB][hapmap]
rs4557909	1.00[CHB][hapmap]
rs4660891	1.00[CHB][hapmap]
rs4660893	1.00[CHB][hapmap]
rs534534	1.00[CHB][hapmap]
rs55659201	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55951835	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56020747	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56093189	0.92[EUR][1000 genomes]
rs56238114	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56251392	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58692133	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61056720	0.80[EUR][1000 genomes]
rs6429573	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6429579	1.00[CHB][hapmap]
rs6659064	1.00[CHB][hapmap]
rs6662999	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6671239	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6673894	1.00[CHB][hapmap]
rs6674105	1.00[CHB][hapmap]
rs6702764	1.00[CHB][hapmap]
rs72688452	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72688460	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7517111	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7525281	1.00[CHB][hapmap]
rs7541935	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556472	1.00[CHB][hapmap]
rs9429173	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv1010054	chr1:46144479-46320493	Active TSS Weak transcription Enhancers Flanking Active TSS 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	75 gene(s)	inside rSNPs	diseases
8	nsv1006861	chr1:46144479-46417621	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
9	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6662572	MED8	cis	cerebellum	SCAN
rs6662572	CCDC163P	cis	Heart Left Ventricle	GTEx
rs6662572	CCDC163P	cis	Thyroid	GTEx
rs6662572	CCDC163P	cis	Whole Blood	GTEx
rs6662572	CCDC163P	cis	Muscle Skeletal	GTEx
rs6662572	TMEM69	Cis_1M	lymphoblastoid	RTeQTL
rs6662572	CCDC163P	cis	Nerve Tibial	GTEx
rs6662572	CCDC163P	cis	lung	GTEx
rs6662572	CCDC163P	cis	Stomach	GTEx
rs6662572	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs6662572	CCDC163P	cis	Artery Tibial	GTEx
rs6662572	CCDC163P	cis	Esophagus Muscularis	GTEx
rs6662572	CCDC163P	cis	Esophagus Mucosa	GTEx
rs6662572	CCDC163P	cis	Artery Aorta	GTEx
rs6662572	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs6662572	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46125000-46148400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:46125200-46151000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:46126000-46147200	Weak transcription	Thymus	Thymus
4	chr1:46126000-46149000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:46126000-46151000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:46126200-46148600	Weak transcription	Fetal Stomach	stomach
7	chr1:46126400-46151000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:46126600-46150600	Weak transcription	Placenta	Placenta
9	chr1:46126800-46147200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:46134200-46151000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:46136000-46150000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:46137400-46149200	Weak transcription	Esophagus	oesophagus
13	chr1:46140600-46150200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:46140800-46148000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:46140800-46149800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:46140800-46149800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:46141200-46150200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:46142200-46149000	Weak transcription	Right Ventricle	heart
19	chr1:46142400-46147200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:46142400-46150400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:46142600-46150000	Enhancers	Adipose Nuclei	Adipose
22	chr1:46142800-46147800	Enhancers	Brain Anterior Caudate	brain
23	chr1:46142800-46149400	Enhancers	Liver	Liver
24	chr1:46142800-46150800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:46143000-46147400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr1:46143000-46148600	Enhancers	Brain Hippocampus Middle	brain
27	chr1:46143000-46148800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:46143000-46150400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:46143200-46149000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:46143200-46149200	Enhancers	Fetal Intestine Small	intestine
31	chr1:46143200-46149400	Weak transcription	Spleen	Spleen
32	chr1:46143400-46148400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:46143400-46148600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr1:46143400-46149600	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:46143400-46150600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:46143400-46150600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:46143800-46151000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:46144200-46150400	Enhancers	Primary B cells from cord blood	blood
39	chr1:46144200-46150800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr1:46144400-46147000	Enhancers	NHEK	skin
41	chr1:46144400-46150000	Weak transcription	Fetal Brain Female	brain
42	chr1:46144600-46147600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr1:46144600-46147800	Enhancers	Fetal Intestine Large	intestine
44	chr1:46144600-46150000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:46144800-46147600	Enhancers	Primary hematopoietic stem cells	blood
46	chr1:46144800-46147800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:46144800-46148000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr1:46144800-46148400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:46144800-46148800	Enhancers	Fetal Heart	heart
50	chr1:46144800-46148800	Enhancers	Fetal Lung	lung

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