Variant report

Variant	rs6948575
Chromosome Location	chr7:112499924-112499925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112490671..112492879-chr7:112499441..112501891,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1227171	0.84[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1227174	0.81[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1227181	0.95[CEU][hapmap]
rs1227190	0.81[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1238698	0.85[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap]
rs12535487	0.86[TSI][hapmap]
rs12539085	0.93[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs1533851	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1547554	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1718944	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1718948	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1718961	0.87[EUR][1000 genomes]
rs1718967	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796492	0.81[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1796493	0.81[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1796512	0.85[EUR][1000 genomes]
rs1796516	0.81[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1996843	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2396573	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2396574	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2457	0.81[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs2687267	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2708295	0.86[EUR][1000 genomes]
rs2708296	0.82[EUR][1000 genomes]
rs3997335	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3997336	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs494324	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs548994	0.85[EUR][1000 genomes]
rs549688	0.91[GIH][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs552304	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs564494	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs565641	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58858661	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62472532	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6466421	0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs660743	0.95[CEU][hapmap]
rs672911	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs685259	0.93[GIH][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6953522	0.93[GIH][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6967716	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7777973	0.95[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs7785774	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7803405	0.81[CEU][hapmap]
rs821782	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs821783	0.91[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs821785	0.81[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs821787	0.81[CEU][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9969347	1.00[ASW][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv2752144	chr7:112398372-112499924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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	7 gene(s)	inside rSNPs	diseases
3	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv2752145	chr7:112434049-112500049	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1034863	chr7:112434413-112504160	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv5905	chr7:112445425-112521797	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv2754368	chr7:112483049-112588049	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6948575	CAV2	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112468600-112550000	Weak transcription	Aorta	Aorta
2	chr7:112469800-112529000	Weak transcription	Brain Anterior Caudate	brain
3	chr7:112470800-112502800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:112470800-112506800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:112470800-112533200	Weak transcription	HSMM	muscle
6	chr7:112471800-112502000	Weak transcription	Fetal Stomach	stomach
7	chr7:112471800-112511200	Weak transcription	HSMMtube	muscle
8	chr7:112471800-112545200	Weak transcription	Ovary	ovary
9	chr7:112472000-112506400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:112472000-112524600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:112472200-112513200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:112472200-112517800	Weak transcription	Osteobl	bone
13	chr7:112472600-112503200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:112472600-112533200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:112472800-112505400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr7:112478400-112506400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr7:112486200-112506400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:112487200-112503000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:112490000-112504000	Weak transcription	Fetal Thymus	thymus
20	chr7:112490800-112533000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:112491200-112508600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:112492200-112506400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:112492600-112501600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:112492600-112501600	Weak transcription	Primary B cells from cord blood	blood
25	chr7:112492600-112502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:112492600-112505000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:112492600-112508800	Weak transcription	Dnd41	blood
28	chr7:112493000-112504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:112493800-112507800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr7:112493800-112509200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:112494200-112503000	Weak transcription	Primary T cells from cord blood	blood
32	chr7:112494200-112508600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:112494200-112532400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr7:112494400-112506600	Weak transcription	Adipose Nuclei	Adipose
35	chr7:112494400-112506600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:112494400-112508800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:112494600-112503000	Weak transcription	Fetal Lung	lung
38	chr7:112495600-112502000	Weak transcription	Fetal Intestine Small	intestine
39	chr7:112495600-112502800	Weak transcription	Fetal Muscle Leg	muscle
40	chr7:112495600-112508400	Weak transcription	Right Ventricle	heart
41	chr7:112495600-112515000	Weak transcription	Pancreas	Pancrea
42	chr7:112495800-112508400	Weak transcription	Fetal Intestine Large	intestine
43	chr7:112496200-112503400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr7:112496200-112509000	Weak transcription	Spleen	Spleen
45	chr7:112496200-112533400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr7:112496600-112506400	Weak transcription	Left Ventricle	heart
47	chr7:112496600-112506400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr7:112498000-112508600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr7:112498000-112508600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:112498000-112515000	Weak transcription	Gastric	stomach

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