Variant report

Variant	rs12644142
Chromosome Location	chr4:110740865-110740866
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr4:110740760-110740885	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:110739041..110741927-chr4:110742062..110743764,2	MCF-7	breast:
2	chr4:110683032..110685527-chr4:110738470..110740917,2	K562	blood:
3	chr4:110739567..110741609-chr4:110748053..110749745,2	MCF-7	breast:
4	chr4:110739239..110741975-chr4:110896217..110899898,3	MCF-7	breast:
5	chr4:110684027..110686689-chr4:110739417..110742962,3	K562	blood:
6	chr4:110736073..110738614-chr4:110739183..110744192,10	MCF-7	breast:
7	chr4:110740840..110743631-chr4:110750092..110752586,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272795	TF binding region
ENSG00000138798	Chromatin interaction
ENSG00000109534	Chromatin interaction
ENSG00000205403	Chromatin interaction
ENSG00000180245	Chromatin interaction
ENSG00000272795	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10020617	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10022841	0.94[CEU][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10516559	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11098049	0.81[ASN][1000 genomes]
rs12498239	0.86[ASN][1000 genomes]
rs12500239	0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504835	1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508179	0.86[ASN][1000 genomes]
rs12510851	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12513108	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12643147	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13109228	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13112387	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13115969	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs13128244	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs13129185	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13140289	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13141065	0.94[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13150454	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1860130	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2078040	0.94[CEU][hapmap];0.86[ASN][1000 genomes]
rs2347130	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs2347131	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs2347132	0.88[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs2347133	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs34377477	0.83[EUR][1000 genomes]
rs34378309	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34706258	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34717063	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34734592	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35426158	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36101562	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775961	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4353905	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4422417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4610335	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698749	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698750	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4698795	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs62324955	0.83[EUR][1000 genomes]
rs6814655	0.86[ASN][1000 genomes]
rs6814743	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6816185	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6841737	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6842245	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6858351	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7442158	0.89[EUR][1000 genomes]
rs7657133	1.00[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7678178	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7684459	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7698794	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9993509	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12644142	RRH	cis	cerebellum	SCAN
rs12644142	GAR1	cis	cerebellum	SCAN
rs12644142	ENPEP	cis	cerebellum	SCAN
rs12644142	GAR1	cis	parietal	SCAN
rs12644142	RRH	cis	parietal	SCAN
rs12644142	LRIT3	cis	cerebellum	SCAN
rs12644142	CYP2U1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110737600-110743400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:110737600-110745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:110737600-110745800	Weak transcription	Spleen	Spleen
4	chr4:110737600-110770600	Weak transcription	Aorta	Aorta
5	chr4:110737800-110741800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr4:110737800-110743400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:110737800-110746400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:110737800-110746600	Weak transcription	Esophagus	oesophagus
9	chr4:110737800-110748000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:110737800-110753200	Weak transcription	Lung	lung
11	chr4:110738000-110741400	Weak transcription	Primary B cells from cord blood	blood
12	chr4:110738000-110741800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:110738000-110743400	Weak transcription	Fetal Stomach	stomach
14	chr4:110738000-110747200	Weak transcription	Gastric	stomach
15	chr4:110738000-110748400	Weak transcription	Small Intestine	intestine
16	chr4:110738000-110760800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:110738200-110742200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:110738200-110743400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:110738200-110743400	Weak transcription	Thymus	Thymus
20	chr4:110738200-110746400	Weak transcription	Colonic Mucosa	Colon
21	chr4:110738200-110747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:110738400-110741000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:110738400-110741200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:110738400-110741800	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:110738400-110742000	Weak transcription	HSMMtube	muscle
26	chr4:110738400-110743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:110738400-110743400	Weak transcription	Pancreas	Pancrea
28	chr4:110738400-110743400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:110738400-110748000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr4:110738400-110748000	Weak transcription	Ovary	ovary
31	chr4:110738400-110748400	Weak transcription	Right Ventricle	heart
32	chr4:110738400-110748600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:110738400-110757200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:110738600-110741000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:110738600-110741200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:110738600-110743600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr4:110738600-110746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:110738600-110747000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:110738600-110747600	Weak transcription	Fetal Heart	heart
40	chr4:110738600-110748400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:110738800-110741000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:110738800-110741400	Weak transcription	Brain Angular Gyrus	brain
43	chr4:110738800-110741400	Weak transcription	Brain Substantia Nigra	brain
44	chr4:110738800-110741800	Weak transcription	Brain Anterior Caudate	brain
45	chr4:110738800-110742600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:110738800-110742600	Strong transcription	Psoas Muscle	Psoas
47	chr4:110738800-110744600	Strong transcription	A549	lung
48	chr4:110738800-110746800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:110738800-110746800	Strong transcription	Adipose Nuclei	Adipose
50	chr4:110738800-110747000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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