Variant report

Variant	rs158796
Chromosome Location	chr5:36878780-36878781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:36877079..36878828-chr5:36943978..36945931,2	MCF-7	breast:
2	chr5:36877699..36879526-chr5:36890759..36893139,2	MCF-7	breast:
3	chr5:36836454..36838672-chr5:36877246..36879256,2	K562	blood:
4	chr5:36877627..36879271-chr5:36903588..36906365,2	MCF-7	breast:
5	chr5:36722181..36727364-chr5:36874838..36878996,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250155	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12657771	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13158310	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13170811	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13176880	0.84[EUR][1000 genomes]
rs13180309	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1466862	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs150380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151944	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs158622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158623	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158624	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158791	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[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159749	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs159751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs159753	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs159755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs159913	0.88[EUR][1000 genomes]
rs168662	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[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs184182	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs186173	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs188488	0.86[AMR][1000 genomes]
rs188541	0.86[EUR][1000 genomes]
rs292172	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs292182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs292183	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs292184	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs292194	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs292195	1.00[CEU][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs296962	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs300049	0.84[EUR][1000 genomes]
rs300051	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs300053	0.86[EUR][1000 genomes]
rs300055	0.87[EUR][1000 genomes]
rs300058	0.88[EUR][1000 genomes]
rs300060	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs300061	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs300063	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs300064	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs300065	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs301859	0.87[EUR][1000 genomes]
rs301901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs301917	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3104057	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs388098	0.87[EUR][1000 genomes]
rs6875748	0.89[EUR][1000 genomes]
rs6899155	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv532133	chr5:36834932-36906436	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs158796	NIPBL	cis	multi-tissue	Pritchard
rs158796	RXFP3	cis	cerebellum	SCAN
rs158796	XM_086879	trans	multi-tissue	Pritchard
rs158796	RPL37	cis	parietal	SCAN
rs158796	LMBRD2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36872800-36881400	Active TSS	GM12878-XiMat	blood
2	chr5:36873400-36879400	Active TSS	Ovary	ovary
3	chr5:36874000-36878800	Active TSS	Psoas Muscle	Psoas
4	chr5:36874000-36879400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:36874000-36879400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr5:36874000-36879400	Active TSS	Right Atrium	heart
7	chr5:36874200-36879200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:36874200-36879800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:36874400-36879800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:36874400-36880000	Active TSS	Fetal Brain Female	brain
11	chr5:36874600-36879200	Active TSS	Fetal Muscle Trunk	muscle
12	chr5:36874600-36879400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr5:36874600-36879400	Active TSS	Fetal Muscle Leg	muscle
14	chr5:36874600-36879400	Active TSS	Right Ventricle	heart
15	chr5:36874600-36879600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:36874600-36879800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:36874800-36878800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr5:36874800-36878800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:36874800-36879000	Active TSS	Left Ventricle	heart
20	chr5:36874800-36879200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:36874800-36879200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr5:36874800-36879400	Active TSS	Aorta	Aorta
23	chr5:36874800-36879600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:36874800-36879600	Active TSS	HSMMtube	muscle
25	chr5:36874800-36879800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:36874800-36879800	Active TSS	NHDF-Ad	bronchial
27	chr5:36874800-36880400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:36874800-36881000	Active TSS	K562	blood
29	chr5:36875000-36878800	Active TSS	Brain Angular Gyrus	brain
30	chr5:36875000-36879400	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr5:36875000-36879400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:36875000-36879400	Active TSS	Fetal Intestine Small	intestine
33	chr5:36875000-36879400	Active TSS	Fetal Stomach	stomach
34	chr5:36875000-36879400	Active TSS	HSMM	muscle
35	chr5:36875000-36879600	Active TSS	Muscle Satellite Cultured Cells	--
36	chr5:36875000-36879800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:36875000-36879800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr5:36875000-36880000	Active TSS	NHLF	lung
39	chr5:36875000-36880600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr5:36875000-36881000	Active TSS	HMEC	breast
41	chr5:36875200-36878800	Active TSS	Brain Cingulate Gyrus	brain
42	chr5:36875200-36878800	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr5:36875200-36879000	Active TSS	Esophagus	oesophagus
44	chr5:36875200-36879000	Active TSS	Placenta	Placenta
45	chr5:36875200-36879200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr5:36875200-36879200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:36875200-36879200	Active TSS	Colon Smooth Muscle	Colon
48	chr5:36875200-36879200	Active TSS	Fetal Kidney	kidney
49	chr5:36875200-36879400	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr5:36875200-36879600	Active TSS	A549	lung

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