Variant report

Variant	rs4730250
Chromosome Location	chr7:107207695-107207696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:107207626-107207995	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:107204495..107206045-chr7:107206098..107207701,2	MCF-7	breast:
2	chr7:107207110..107210037-chr7:107211935..107213568,2	MCF-7	breast:
3	chr7:107202748..107209925-chr7:107217558..107222659,11	MCF-7	breast:

Variant related genes	Relation type
COG5	TF binding region
DUS4L	TF binding region
ENSG00000075790	Chromatin interaction
ENSG00000164597	Chromatin interaction
ENSG00000272854	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10464499	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10464620	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]
rs10953541	0.94[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11532774	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11766131	0.84[ASN][1000 genomes]
rs11770061	0.84[ASN][1000 genomes]
rs12056231	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12533694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12534124	0.89[ASN][1000 genomes]
rs12535038	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12535761	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]
rs12539895	0.88[ASN][1000 genomes]
rs13234124	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17403088	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17404067	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17481621	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17481842	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17482494	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17482543	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17486	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1978085	0.89[ASN][1000 genomes]
rs2283041	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299428	0.90[ASN][1000 genomes]
rs2395880	0.84[ASN][1000 genomes]
rs2395881	0.84[ASN][1000 genomes]
rs34084719	0.89[ASN][1000 genomes]
rs34523267	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3779497	0.85[ASN][1000 genomes]
rs4515482	0.84[ASN][1000 genomes]
rs4727683	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4730248	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs56949084	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6943051	0.81[MEX][hapmap];1.00[MKK][hapmap]
rs6945784	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6947674	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6955488	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6957186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6958969	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6964395	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6976759	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6979198	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6979368	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs763386	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[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7784906	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7785085	0.88[AMR][1000 genomes]
rs7785962	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7797791	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7801317	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7807154	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8180747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv608074	chr7:107179131-107260856	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Osteoarthritis	21068099	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4730250	HBP1	cis	cerebellum	SCAN
rs4730250	NRCAM	cis	parietal	SCAN
rs4730250	PRKAR2B	cis	cerebellum	SCAN
rs4730250	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107204800-107210600	Weak transcription	Spleen	Spleen
2	chr7:107205000-107210600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:107205000-107219600	Weak transcription	Pancreas	Pancrea
4	chr7:107205000-107220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:107205000-107220000	Weak transcription	Gastric	stomach
6	chr7:107205000-107220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:107205000-107220200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:107205200-107210400	Weak transcription	Fetal Thymus	thymus
9	chr7:107205200-107210600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr7:107205200-107210600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:107205200-107210600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:107205200-107210600	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:107205200-107210600	Weak transcription	Placenta	Placenta
14	chr7:107205200-107210600	Weak transcription	Left Ventricle	heart
15	chr7:107205200-107210800	Weak transcription	Ovary	ovary
16	chr7:107205200-107219600	Weak transcription	Esophagus	oesophagus
17	chr7:107205200-107219600	Weak transcription	Right Ventricle	heart
18	chr7:107205200-107220000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:107205200-107220000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:107205200-107220000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:107205200-107220000	Weak transcription	Lung	lung
22	chr7:107205200-107220000	Weak transcription	Psoas Muscle	Psoas
23	chr7:107205400-107210600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr7:107205400-107210800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:107205400-107211800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:107205400-107219800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:107205400-107220000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr7:107205400-107220000	Weak transcription	Colonic Mucosa	Colon
29	chr7:107205400-107220000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr7:107205600-107208000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:107205600-107210000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:107205600-107210000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:107205600-107210200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:107205600-107210400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:107205600-107210400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr7:107205600-107210600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:107205600-107210600	Weak transcription	Fetal Brain Female	brain
38	chr7:107205600-107210800	Weak transcription	Adipose Nuclei	Adipose
39	chr7:107205600-107210800	Weak transcription	Liver	Liver
40	chr7:107205600-107210800	Weak transcription	Fetal Intestine Large	intestine
41	chr7:107205600-107211600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr7:107205600-107211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:107205600-107211800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:107205600-107211800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr7:107205600-107214000	Weak transcription	Small Intestine	intestine
46	chr7:107205600-107215200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:107205600-107215400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:107205600-107215400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr7:107205600-107219600	Weak transcription	Aorta	Aorta
50	chr7:107205600-107219600	Weak transcription	Fetal Stomach	stomach

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