Variant report

Variant	rs6592
Chromosome Location	chr7:99668107-99668108
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99510858..99512845-chr7:99666922..99668822,2	K562	blood:
2	chr7:99666965..99668783-chr7:99673527..99675270,2	MCF-7	breast:
3	chr7:99667576..99670225-chr7:99671160..99673270,2	MCF-7	breast:
4	chr7:99661987..99666406-chr7:99667743..99671681,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166526	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11558475	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11558476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673441	0.90[MEX][hapmap];0.93[MKK][hapmap];0.82[ASN][1000 genomes]
rs2261360	0.90[MEX][hapmap];0.86[MKK][hapmap]
rs4308665	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4421299	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4729573	0.81[ASN][1000 genomes]
rs4729575	0.82[JPT][hapmap];0.86[MKK][hapmap]
rs55969052	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56054049	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60697181	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67091024	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67110214	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68038211	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72615158	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72615159	0.82[ASN][1000 genomes]
rs7780686	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7796006	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7803317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941289	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6592	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs6592	PILRB	cis	parietal	SCAN
rs6592	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs6592	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs6592	OR2AE1	cis	parietal	SCAN
rs6592	MUC17	cis	parietal	SCAN
rs6592	MCM7	cis	parietal	SCAN
rs6592	MBLAC1	cis	cerebellum	SCAN
rs6592	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs6592	AP4M1	cis	cerebellum	SCAN
rs6592	LOC389541	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99654400-99668400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:99661600-99675200	ZNF genes & repeats	A549	lung
3	chr7:99662200-99668400	Weak transcription	Small Intestine	intestine
4	chr7:99664600-99673600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:99664800-99668400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:99665600-99668600	Strong transcription	Brain Hippocampus Middle	brain
7	chr7:99665800-99673400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:99665800-99673600	ZNF genes & repeats	Fetal Stomach	stomach
9	chr7:99666000-99675000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
10	chr7:99666200-99668200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr7:99666400-99668600	Strong transcription	Brain Angular Gyrus	brain
12	chr7:99666400-99674000	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr7:99666400-99677200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:99666400-99678000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:99666600-99668600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:99666600-99672000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:99666600-99674000	ZNF genes & repeats	Fetal Muscle Leg	muscle
18	chr7:99666800-99668400	Strong transcription	Ovary	ovary
19	chr7:99666800-99672000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:99666800-99673400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
21	chr7:99666800-99673600	ZNF genes & repeats	HSMM	muscle
22	chr7:99666800-99673800	ZNF genes & repeats	GM12878-XiMat	blood
23	chr7:99666800-99674400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr7:99666800-99675200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr7:99666800-99677000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:99667000-99668200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:99667000-99668200	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr7:99667000-99668200	Strong transcription	HSMMtube	muscle
29	chr7:99667000-99668400	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:99667000-99668400	Strong transcription	Gastric	stomach
31	chr7:99667000-99668400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr7:99667000-99668400	Strong transcription	Dnd41	blood
33	chr7:99667000-99668800	Strong transcription	Pancreas	Pancrea
34	chr7:99667000-99671000	ZNF genes & repeats	NHLF	lung
35	chr7:99667000-99673400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
36	chr7:99667000-99673600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr7:99667200-99668400	Strong transcription	Colon Smooth Muscle	Colon
38	chr7:99667200-99670400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:99667200-99671000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
40	chr7:99667200-99671000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:99667200-99671400	ZNF genes & repeats	Lung	lung
42	chr7:99667200-99671800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
43	chr7:99667200-99673000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr7:99667200-99673200	ZNF genes & repeats	Fetal Intestine Large	intestine
45	chr7:99667400-99668200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr7:99667400-99668400	Strong transcription	Brain Anterior Caudate	brain
47	chr7:99667400-99668400	Strong transcription	Brain Cingulate Gyrus	brain
48	chr7:99667400-99668400	Strong transcription	Pancreatic Islets	Pancreatic Islet
49	chr7:99667400-99668600	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr7:99667400-99669800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood

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