Variant report

Variant	rs6492721
Chromosome Location	chr13:95258944-95258945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95253610..95255807-chr13:95256426..95259673,3	MCF-7	breast:
2	chr13:95258888..95260648-chr13:95263620..95266096,2	K562	blood:
3	chr13:95258888..95261830-chr13:95264596..95266562,2	K562	blood:
4	chr13:95246788..95248667-chr13:95257874..95259560,2	MCF-7	breast:
5	chr13:95253721..95257093-chr13:95258270..95263356,4	K562	blood:

Variant related genes	Relation type
ENSG00000152749	Chromatin interaction
ENSG00000088451	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1341267	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1572935	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2275647	0.82[GIH][hapmap]
rs2298055	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2298056	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2298057	0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2298058	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35253817	0.99[ASN][1000 genomes]
rs3897473	0.98[ASN][1000 genomes]
rs3897474	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4238308	0.97[ASN][1000 genomes]
rs4296139	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4465476	0.91[ASN][1000 genomes]
rs4771890	0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs6492720	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492723	0.97[ASN][1000 genomes]
rs6492725	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7326576	0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7981788	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9516445	0.98[ASN][1000 genomes]
rs9516448	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9524555	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9524556	0.98[ASN][1000 genomes]
rs9524557	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9524559	0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs9524561	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs9524566	0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9524568	0.89[ASN][1000 genomes]
rs9556404	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9556405	0.90[ASN][1000 genomes]
rs9561643	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561645	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6492721	GPR180	cis	multi-tissue	Pritchard
rs6492721	UGGT2	cis	parietal	SCAN
rs6492721	ITR	cis	multi-tissue	Pritchard
rs6492721	GPR180	cis	Liver	GTEx
rs6492721	GPR180	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254600-95259200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:95254600-95276600	Weak transcription	Small Intestine	intestine
3	chr13:95254600-95284000	Weak transcription	Spleen	Spleen
4	chr13:95254800-95259200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:95254800-95259200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr13:95254800-95259200	Weak transcription	Gastric	stomach
7	chr13:95254800-95263000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr13:95254800-95263800	Weak transcription	Left Ventricle	heart
9	chr13:95254800-95263800	Weak transcription	Pancreas	Pancrea
10	chr13:95254800-95263800	Weak transcription	Psoas Muscle	Psoas
11	chr13:95254800-95268200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr13:95254800-95272000	Weak transcription	Lung	lung
13	chr13:95254800-95275400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr13:95254800-95275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:95255000-95259000	Weak transcription	Ovary	ovary
17	chr13:95255000-95259000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr13:95255000-95259000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr13:95255000-95259400	Weak transcription	Right Atrium	heart
20	chr13:95255000-95260200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr13:95255000-95260400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr13:95255000-95262800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:95255000-95262800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr13:95255000-95263200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr13:95255000-95263200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:95255000-95275400	Weak transcription	Aorta	Aorta
27	chr13:95255000-95275600	Weak transcription	Right Ventricle	heart
28	chr13:95255000-95276200	Weak transcription	HSMMtube	muscle
29	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
30	chr13:95255200-95259200	Weak transcription	Fetal Intestine Large	intestine
31	chr13:95255200-95259400	Weak transcription	Brain Germinal Matrix	brain
32	chr13:95255200-95262000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:95255200-95262800	Weak transcription	Fetal Kidney	kidney
34	chr13:95255200-95272200	Weak transcription	Colon Smooth Muscle	Colon
35	chr13:95255200-95276200	Weak transcription	Fetal Brain Female	brain
36	chr13:95255200-95278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
38	chr13:95255400-95259000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr13:95255400-95259200	Weak transcription	Stomach Mucosa	stomach
40	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr13:95255600-95268000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
43	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
44	chr13:95255800-95259000	Weak transcription	NHLF	lung
45	chr13:95255800-95259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:95255800-95259800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:95255800-95259800	Weak transcription	Brain Anterior Caudate	brain
48	chr13:95255800-95260400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr13:95255800-95260400	Weak transcription	Brain Substantia Nigra	brain
50	chr13:95255800-95261600	Weak transcription	Primary T cells from cord blood	blood

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