Variant report

Variant	rs7808729
Chromosome Location	chr7:56136194-56136195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10043	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10260048	0.82[JPT][hapmap]
rs10263766	0.82[CHB][hapmap]
rs1064337	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238395	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11764629	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11765364	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11772545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12535749	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535872	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs15892	0.82[JPT][hapmap]
rs1894833	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1894834	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2002693	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2080141	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304376	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2538048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2908546	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2908547	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2908548	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2965455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4947528	0.88[CHB][hapmap]
rs4947529	0.88[CHB][hapmap]
rs4948090	0.82[JPT][hapmap]
rs4948093	0.82[JPT][hapmap]
rs55697950	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55863006	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56389944	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457279	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457281	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457282	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457284	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457286	0.82[ASN][1000 genomes]
rs62457287	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457288	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457289	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457291	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6593290	0.88[CHB][hapmap]
rs6593296	1.00[YRI][hapmap]
rs6951202	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6955663	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6965614	0.93[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];0.92[ASN][1000 genomes]
rs6974707	0.88[CHB][hapmap]
rs73140771	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7790255	0.88[CHB][hapmap]
rs7801405	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7811889	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs816410	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9649860	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7808729	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs7808729	LOC146325	trans	lymphoblastoid	RTeQTL
rs7808729	CHCHD2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56131800-56146800	Weak transcription	Fetal Heart	heart
2	chr7:56132400-56141800	Weak transcription	Stomach Mucosa	stomach
3	chr7:56132400-56145400	Weak transcription	Spleen	Spleen
4	chr7:56132600-56136200	Weak transcription	Gastric	stomach
5	chr7:56132600-56136400	Weak transcription	Lung	lung
6	chr7:56132800-56136200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:56132800-56136400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:56133000-56136200	Weak transcription	Aorta	Aorta
9	chr7:56133000-56136600	Weak transcription	Pancreas	Pancrea
10	chr7:56133200-56136200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:56133200-56136200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:56133200-56136200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:56133200-56136200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:56133200-56136200	Weak transcription	Brain Anterior Caudate	brain
15	chr7:56133200-56136200	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:56133200-56136200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:56133200-56136200	Weak transcription	Left Ventricle	heart
18	chr7:56133200-56136200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:56133200-56136200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:56133200-56136200	Weak transcription	HSMMtube	muscle
21	chr7:56133200-56136400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr7:56133200-56136400	Weak transcription	Right Ventricle	heart
23	chr7:56133200-56136600	Weak transcription	Brain Substantia Nigra	brain
24	chr7:56133200-56136600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr7:56133200-56136600	Weak transcription	NH-A	brain
26	chr7:56133200-56138400	Weak transcription	Brain Angular Gyrus	brain
27	chr7:56133200-56138400	Weak transcription	Fetal Kidney	kidney
28	chr7:56133200-56140600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr7:56133200-56141800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:56133200-56141800	Weak transcription	HepG2	liver
31	chr7:56133200-56142000	Weak transcription	Esophagus	oesophagus
32	chr7:56133200-56142200	Weak transcription	Right Atrium	heart
33	chr7:56133200-56145600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:56133200-56146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
36	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
37	chr7:56133400-56136200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr7:56133400-56136200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:56133400-56136200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:56133400-56136200	Weak transcription	Fetal Brain Female	brain
41	chr7:56133400-56136200	Weak transcription	Hela-S3	cervix
42	chr7:56133400-56136200	Weak transcription	Osteobl	bone
43	chr7:56133400-56136400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:56133400-56136400	Weak transcription	Brain Germinal Matrix	brain
45	chr7:56133400-56138000	Weak transcription	HMEC	breast
46	chr7:56133400-56138400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:56133400-56144200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr7:56133400-56145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:56133600-56136200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:56133600-56136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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