Variant report

Variant	rs13125082
Chromosome Location	chr4:57787000-57787001
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57772930..57780141-chr4:57782916..57788353,10	K562	blood:
2	chr4:57778640..57781071-chr4:57785641..57787696,2	K562	blood:
3	chr4:57785111..57787952-chr4:57797814..57799523,2	K562	blood:

Variant related genes	Relation type
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10016108	1.00[CHB][hapmap]
rs1107674	0.80[CEU][hapmap]
rs11133472	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11573041	1.00[CHB][hapmap]
rs11573128	1.00[CHB][hapmap]
rs11721387	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11726410	1.00[ASN][1000 genomes]
rs11726443	1.00[ASN][1000 genomes]
rs11726548	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11727329	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731657	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11732394	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs13113032	0.86[EUR][1000 genomes]
rs13116564	0.80[EUR][1000 genomes]
rs13123018	0.92[ASN][1000 genomes]
rs13128671	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13130600	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130604	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13146090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs13146153	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs13152711	0.82[EUR][1000 genomes]
rs1618761	1.00[CHB][hapmap]
rs17087358	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs17183291	1.00[CHB][hapmap]
rs1718846	1.00[CHB][hapmap]
rs1718848	1.00[CHB][hapmap]
rs2002153	0.80[EUR][1000 genomes]
rs2412761	1.00[ASN][1000 genomes]
rs34308849	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34840470	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34937594	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35185186	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35318869	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4109037	1.00[CHB][hapmap]
rs41495551	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs4413466	1.00[ASN][1000 genomes]
rs4443350	1.00[ASN][1000 genomes]
rs4864606	0.83[EUR][1000 genomes]
rs4865166	0.85[EUR][1000 genomes]
rs4865176	1.00[CHB][hapmap]
rs4865177	1.00[CHB][hapmap]
rs55822707	0.81[EUR][1000 genomes]
rs56143151	1.00[ASN][1000 genomes]
rs62308068	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62308099	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62308100	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62308107	0.91[ASN][1000 genomes]
rs62308135	0.83[EUR][1000 genomes]
rs62308136	0.83[EUR][1000 genomes]
rs62308153	1.00[ASN][1000 genomes]
rs66619445	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6839166	1.00[ASN][1000 genomes]
rs729844	0.80[EUR][1000 genomes]
rs73242609	0.84[EUR][1000 genomes]
rs7656865	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7661194	0.82[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs7684642	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7685053	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9055	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9760540	1.00[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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3425352	chr4:57783591-57820951	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1797793	chr4:57786450-57793425	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13125082	POLR2B	cis	cerebellum	SCAN
rs13125082	RP11-738E22.3	cis	Esophagus Mucosa	GTEx
rs13125082	RP11-738E22.3	cis	Thyroid	GTEx
rs13125082	IGFBP7	cis	multi-tissue	Pritchard
rs13125082	TXNDC9	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57776400-57789400	Weak transcription	Right Ventricle	heart
2	chr4:57777000-57795800	Weak transcription	A549	lung
3	chr4:57777000-57796600	Weak transcription	Fetal Brain Female	brain
4	chr4:57777000-57797000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:57777200-57793400	Weak transcription	HMEC	breast
6	chr4:57777200-57796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:57777200-57796600	Weak transcription	Aorta	Aorta
8	chr4:57777200-57796800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:57777200-57797200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:57777600-57796000	Weak transcription	Brain Anterior Caudate	brain
11	chr4:57777600-57796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:57777600-57796600	Weak transcription	Colonic Mucosa	Colon
13	chr4:57777600-57803200	Weak transcription	NHDF-Ad	bronchial
14	chr4:57777600-57805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:57777600-57806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:57778000-57791800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:57778000-57796000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:57778000-57796000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:57778000-57796600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:57778000-57797000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:57778200-57796200	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:57778200-57796800	Weak transcription	NHLF	lung
23	chr4:57778400-57788600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:57778400-57795400	Weak transcription	HSMMtube	muscle
25	chr4:57778400-57796000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:57778400-57800200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:57778400-57800200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:57778400-57801000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:57778800-57795800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:57779000-57804600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:57779200-57799200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:57779800-57789600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:57779800-57796000	Weak transcription	Small Intestine	intestine
34	chr4:57779800-57797600	Weak transcription	Fetal Brain Male	brain
35	chr4:57779800-57799600	Weak transcription	Right Atrium	heart
36	chr4:57780200-57793000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:57780400-57800400	Strong transcription	Fetal Thymus	thymus
38	chr4:57780800-57795600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:57780800-57808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:57781000-57791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:57781000-57796800	Weak transcription	Spleen	Spleen
42	chr4:57781000-57799600	Weak transcription	Psoas Muscle	Psoas
43	chr4:57781800-57801400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:57782200-57788000	Weak transcription	NHEK	skin
45	chr4:57782200-57790800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:57782400-57792400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:57782400-57796000	Weak transcription	Hela-S3	cervix
48	chr4:57782800-57792600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:57782800-57796800	Weak transcription	Pancreas	Pancrea
50	chr4:57783000-57787400	Strong transcription	H1 Cell Line	embryonic stem cell

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