Variant report

Variant	rs6593290
Chromosome Location	chr7:55974939-55974940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10043	0.85[CHB][hapmap]
rs10236322	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10260031	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10260048	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10263766	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238384	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11238392	0.88[CHB][hapmap]
rs11238393	0.85[CHB][hapmap]
rs11765364	1.00[ASW][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap]
rs11771756	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12538444	0.86[CHB][hapmap]
rs13230292	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13240729	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs15892	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1967230	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304376	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2331096	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331166	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2538048	1.00[ASW][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap]
rs35347591	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4245574	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4518614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4948090	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4948093	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4948094	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56128104	0.82[AMR][1000 genomes]
rs56207001	0.85[AMR][1000 genomes]
rs56269128	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56351949	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62456630	0.83[ASN][1000 genomes]
rs62456648	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62456651	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62456653	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62456654	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6421738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945638	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs6946065	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6965614	0.88[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs6970353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6972415	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6974707	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7778138	0.83[ASN][1000 genomes]
rs7790255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7808729	0.88[CHB][hapmap]
rs816407	1.00[ASW][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap]
rs8406	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs9649783	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv427782	chr7:55703073-56010314	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv607034	chr7:55974028-56002247	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6593290	GBAS	cis	parietal	SCAN
rs6593290	CHCHD2	cis	parietal	SCAN
rs6593290	CHCHD2	cis	multi-tissue	Pritchard
rs6593290	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs6593290	ZNF713	cis	cerebellum	SCAN
rs6593290	CHCHD2	cis	cerebellum	SCAN
rs6593290	LOC146325	trans	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55955400-56004200	Weak transcription	Gastric	stomach
2	chr7:55955800-55975000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:55955800-55985800	Weak transcription	Esophagus	oesophagus
4	chr7:55956000-55979600	Weak transcription	Psoas Muscle	Psoas
5	chr7:55956200-55975200	Weak transcription	HSMMtube	muscle
6	chr7:55956200-55979400	Weak transcription	Primary T cells from cord blood	blood
7	chr7:55956200-55979600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:55956200-55990800	Weak transcription	Thymus	Thymus
9	chr7:55956200-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:55956400-55975000	Weak transcription	Liver	Liver
11	chr7:55956400-55979000	Weak transcription	Brain Substantia Nigra	brain
12	chr7:55956400-55979600	Weak transcription	Brain Angular Gyrus	brain
13	chr7:55956400-55979800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:55956400-55990600	Weak transcription	Brain Anterior Caudate	brain
15	chr7:55956400-55995800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:55956400-55998800	Weak transcription	Colon Smooth Muscle	Colon
17	chr7:55956600-55979400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:55956600-55990800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:55961800-55979400	Weak transcription	Spleen	Spleen
20	chr7:55962000-55990000	Weak transcription	HepG2	liver
21	chr7:55962000-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:55962600-55977800	Weak transcription	Fetal Heart	heart
23	chr7:55966600-55983800	Weak transcription	HUVEC	blood vessel
24	chr7:55966800-55979600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr7:55967600-55995800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr7:55968000-55975200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:55968200-55975200	Weak transcription	Fetal Intestine Small	intestine
28	chr7:55968600-55995000	Weak transcription	HSMM	muscle
29	chr7:55969000-55975000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:55969000-55985600	Weak transcription	Dnd41	blood
31	chr7:55969600-55975000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:55969600-55979400	Weak transcription	Lung	lung
33	chr7:55969800-55979000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr7:55969800-55998200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:55971600-55993400	Weak transcription	Primary B cells from cord blood	blood
36	chr7:55971800-55980200	Weak transcription	Right Ventricle	heart
37	chr7:55971800-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:55973000-55975000	Strong transcription	Fetal Stomach	stomach
39	chr7:55973000-55975600	Strong transcription	Fetal Lung	lung
40	chr7:55973600-55990800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:55973800-55975000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:55973800-55975000	Strong transcription	Fetal Intestine Large	intestine
43	chr7:55973800-55975400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr7:55973800-55975400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr7:55973800-55975400	Strong transcription	Left Ventricle	heart
46	chr7:55973800-55975600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr7:55973800-55979600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr7:55974000-55975000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr7:55974000-55975400	Strong transcription	Ovary	ovary
50	chr7:55974000-55975600	Strong transcription	Fetal Muscle Leg	muscle

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