Variant report

Variant	rs12535761
Chromosome Location	chr7:107139275-107139276
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107134045..107136740-chr7:107137894..107140171,2	MCF-7	breast:
2	chr7:107136433..107141065-chr7:107144603..107148150,5	MCF-7	breast:
3	chr7:107120115..107121857-chr7:107137628..107139612,2	K562	blood:

Variant related genes	Relation type
ENSG00000164597	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10464499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464620	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]
rs10953541	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs11532774	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11766131	0.88[ASN][1000 genomes]
rs11770061	0.88[ASN][1000 genomes]
rs12056231	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12532447	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12532849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12533694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12534124	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12535038	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12539895	0.92[ASN][1000 genomes]
rs13234124	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs17403088	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17404067	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17481842	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17482494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17482543	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978085	0.93[ASN][1000 genomes]
rs2249043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2283041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299428	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395880	0.88[ASN][1000 genomes]
rs2395881	0.88[ASN][1000 genomes]
rs2894459	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs34084719	0.93[ASN][1000 genomes]
rs34523267	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3779497	0.89[ASN][1000 genomes]
rs4515482	0.88[ASN][1000 genomes]
rs4727683	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730248	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56949084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6945784	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6947674	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6964395	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6976759	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979198	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6979368	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs763386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7784906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785085	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7785962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs7797791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7801317	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807154	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12535761	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 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	chr7:107135600-107145800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:107135600-107146000	Weak transcription	NHLF	lung
28	chr7:107135800-107145600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr7:107136000-107165800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr7:107136200-107145200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:107136200-107148000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr7:107137000-107166200	Weak transcription	K562	blood
33	chr7:107137800-107142600	Enhancers	Fetal Heart	heart
34	chr7:107138000-107145600	Weak transcription	Fetal Intestine Small	intestine
35	chr7:107138400-107149200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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