Variant report

Variant	rs10464620
Chromosome Location	chr7:107135653-107135654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107134560..107137629-chr7:107140496..107142146,3	K562	blood:
2	chr7:107134186..107135883-chr7:107215334..107217413,2	K562	blood:
3	chr7:107134045..107136740-chr7:107137894..107140171,2	MCF-7	breast:
4	chr7:107129731..107132088-chr7:107135002..107137252,2	MCF-7	breast:
5	chr7:107116237..107119401-chr7:107133412..107136186,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105865	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10464499	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953541	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11532774	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11762604	1.00[LWK][hapmap]
rs11766131	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11770061	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12056231	0.93[ASN][1000 genomes]
rs12532447	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12532849	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12533694	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12534124	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12535038	0.92[ASN][1000 genomes]
rs12535258	0.94[CEU][hapmap]
rs12535761	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539895	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13234124	0.89[ASN][1000 genomes]
rs17403088	0.86[CEU][hapmap];0.93[CHB][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17404067	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481621	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17481842	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17482494	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17482543	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17486	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978085	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2249043	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs2283041	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2299428	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395880	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395881	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2894459	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs34084719	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34523267	0.89[ASN][1000 genomes]
rs3779497	0.89[ASN][1000 genomes]
rs4515482	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4727683	0.93[ASN][1000 genomes]
rs4730239	0.81[EUR][1000 genomes]
rs4730241	0.81[EUR][1000 genomes]
rs4730242	0.81[EUR][1000 genomes]
rs4730248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730250	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs56949084	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6945784	0.97[ASN][1000 genomes]
rs6947674	0.93[ASN][1000 genomes]
rs6955488	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957186	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6958969	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6964395	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6976759	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979198	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6979368	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs763386	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7784906	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7797791	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7801317	1.00[ASN][1000 genomes]
rs7807154	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180747	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][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	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv1019963	chr7:107033342-107188641	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv539052	chr7:107033342-107188641	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv482365	chr7:107122401-107271861	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10464620	PRKAR2B	cis	cerebellum	SCAN
rs10464620	ATXN7L1	cis	cerebellum	SCAN
rs10464620	GPR22	cis	multi-tissue	Pritchard
rs10464620	GPR22	Cis_1M	lymphoblastoid	RTeQTL
rs10464620	COG5	cis	parietal	SCAN
rs10464620	NRCAM	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107090800-107146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:107091000-107145800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr7:107112800-107145800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr7:107120000-107145600	Weak transcription	Right Ventricle	heart
5	chr7:107122000-107147000	Weak transcription	HSMM	muscle
6	chr7:107123200-107155800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:107123600-107166200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr7:107126600-107145600	Weak transcription	Adipose Nuclei	Adipose
9	chr7:107126800-107184800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:107127400-107175400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:107130800-107145400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr7:107130800-107163400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:107131400-107179800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:107131800-107146000	Weak transcription	Dnd41	blood
15	chr7:107131800-107175000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr7:107132000-107146200	Weak transcription	Colonic Mucosa	Colon
17	chr7:107132000-107146800	Weak transcription	Fetal Thymus	thymus
18	chr7:107132200-107146400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:107132200-107146800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:107133200-107140200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:107133200-107145600	Weak transcription	Aorta	Aorta
22	chr7:107133600-107145400	Weak transcription	Primary T cells from cord blood	blood
23	chr7:107133600-107145600	Weak transcription	Primary B cells from cord blood	blood
24	chr7:107133600-107146800	Weak transcription	Right Atrium	heart
25	chr7:107133800-107144400	Weak transcription	Psoas Muscle	Psoas
26	chr7:107134600-107135800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr7:107134600-107136200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:107135200-107135800	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr7:107135200-107135800	Enhancers	Left Ventricle	heart
30	chr7:107135200-107135800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr7:107135400-107135800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr7:107135400-107136200	Flanking Active TSS	K562	blood
33	chr7:107135600-107135800	Enhancers	Pancreas	Pancrea
34	chr7:107135600-107136200	Enhancers	Fetal Heart	heart
35	chr7:107135600-107145800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:107135600-107146000	Weak transcription	NHLF	lung

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