Variant report

Variant	rs6593292
Chromosome Location	chr7:56043037-56043038
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56042947..56046138-chr7:56046396..56049089,4	K562	blood:
2	chr7:56034811..56036725-chr7:56042594..56044102,2	K562	blood:

Variant related genes	Relation type
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10223916	0.81[JPT][hapmap]
rs10229446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10230845	0.81[JPT][hapmap]
rs10233558	0.81[JPT][hapmap]
rs10245725	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10250964	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10252442	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10266902	0.88[ASN][1000 genomes]
rs10271662	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10272406	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10277978	0.82[JPT][hapmap]
rs10435504	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238389	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11761352	0.86[JPT][hapmap]
rs11765287	0.82[JPT][hapmap]
rs11765531	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11765577	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13240915	0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs13241866	0.85[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs13245637	0.85[YRI][hapmap]
rs2135116	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2174461	0.86[JPT][hapmap]
rs28636652	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28678267	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28803557	0.81[JPT][hapmap]
rs28828764	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34016595	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35844144	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275190	0.89[YRI][hapmap]
rs4470984	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4947533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4947534	0.85[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4948096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948097	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4948099	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4948102	0.86[CHB][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs57153841	0.89[ASN][1000 genomes]
rs57251705	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs60517461	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6593294	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6593297	0.88[YRI][hapmap]
rs66528253	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6943341	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs6954499	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955423	0.84[EUR][1000 genomes]
rs6978852	0.81[JPT][hapmap]
rs73132854	0.89[ASN][1000 genomes]
rs73132897	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73360358	0.95[ASN][1000 genomes]
rs73360359	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7776550	0.82[EUR][1000 genomes]
rs7779394	0.81[JPT][hapmap]
rs7800001	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7811755	0.85[EUR][1000 genomes]
rs9642405	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers 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	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers 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	46 gene(s)	inside rSNPs	diseases
6	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6593292	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs6593292	GBAS	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56033200-56045400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:56033200-56045600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:56033200-56045600	Weak transcription	Aorta	Aorta
4	chr7:56033200-56045800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr7:56033200-56048600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:56033200-56050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:56033200-56081400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:56033400-56045200	Weak transcription	HUVEC	blood vessel
9	chr7:56033400-56045600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:56033400-56045600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr7:56033400-56047000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:56033400-56047600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:56033600-56045600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:56033800-56045400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:56033800-56045400	Weak transcription	Hela-S3	cervix
16	chr7:56033800-56045400	Weak transcription	HSMM	muscle
17	chr7:56033800-56045600	Weak transcription	Placenta	Placenta
18	chr7:56033800-56045800	Weak transcription	Fetal Thymus	thymus
19	chr7:56033800-56045800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:56033800-56046000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:56033800-56046800	Weak transcription	GM12878-XiMat	blood
22	chr7:56033800-56046800	Weak transcription	NHLF	lung
23	chr7:56033800-56047200	Weak transcription	Colonic Mucosa	Colon
24	chr7:56033800-56047800	Weak transcription	HMEC	breast
25	chr7:56033800-56063000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:56033800-56065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:56034000-56045400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:56034000-56045400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:56034000-56045600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:56034000-56046000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:56034000-56046200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:56034000-56046400	Weak transcription	Fetal Kidney	kidney
33	chr7:56034000-56046800	Weak transcription	NHEK	skin
34	chr7:56034200-56045400	Weak transcription	Liver	Liver
35	chr7:56034200-56046000	Weak transcription	K562	blood
36	chr7:56034600-56045200	Weak transcription	Fetal Brain Male	brain
37	chr7:56034600-56045400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr7:56034600-56046000	Weak transcription	NHDF-Ad	bronchial
39	chr7:56034800-56044200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:56034800-56045400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr7:56034800-56045800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:56035000-56045200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:56035000-56045200	Weak transcription	Brain Germinal Matrix	brain
44	chr7:56035000-56045600	Weak transcription	HepG2	liver
45	chr7:56035000-56046200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:56036600-56045400	Weak transcription	Fetal Lung	lung
47	chr7:56037400-56045000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:56037400-56045400	Weak transcription	Colon Smooth Muscle	Colon
49	chr7:56037400-56045400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:56037400-56045400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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