Variant report

Variant	rs35253817
Chromosome Location	chr13:95258242-95258243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95253610..95255807-chr13:95256426..95259673,3	MCF-7	breast:
2	chr13:95246788..95248667-chr13:95257874..95259560,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152749	Chromatin interaction
ENSG00000088451	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1112370	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1341267	0.91[ASN][1000 genomes]
rs1408999	0.82[EUR][1000 genomes]
rs1572935	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2275648	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2298055	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2298056	0.91[ASN][1000 genomes]
rs2298057	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs34350725	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34405130	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3742107	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3897473	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3897474	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238308	0.96[ASN][1000 genomes]
rs4296139	0.96[ASN][1000 genomes]
rs4465476	0.90[ASN][1000 genomes]
rs4473052	0.83[EUR][1000 genomes]
rs4608209	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4771890	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4773801	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492716	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492718	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492720	0.98[ASN][1000 genomes]
rs6492721	0.99[ASN][1000 genomes]
rs6492723	0.96[ASN][1000 genomes]
rs6492725	0.91[ASN][1000 genomes]
rs7321239	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7326576	0.91[ASN][1000 genomes]
rs7330873	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7331814	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7339106	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7981788	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7991607	0.81[EUR][1000 genomes]
rs7997035	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7997333	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7998025	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9301979	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9301981	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9301983	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9516437	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9516438	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9516440	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9516441	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9516443	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9516445	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516448	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9524544	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524545	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524547	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9524548	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524549	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524550	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524551	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524553	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524554	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9524555	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524556	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524557	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524559	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524560	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9524561	0.88[AFR][1000 genomes]
rs9524562	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9524563	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9524566	0.93[ASN][1000 genomes]
rs9524568	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9556402	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9556405	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9561642	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9561643	0.91[ASN][1000 genomes]
rs9561645	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9590037	0.88[AMR][1000 genomes];0.90[EUR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs35253817	GPR180	cis	Artery Tibial	GTEx
rs35253817	GPR180	cis	Stomach	GTEx
rs35253817	GPR180	cis	Adipose Subcutaneous	GTEx
rs35253817	GPR180	cis	lung	GTEx
rs35253817	GPR180	cis	Esophagus Mucosa	GTEx
rs35253817	GPR180	cis	Muscle Skeletal	GTEx
rs35253817	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs35253817	GPR180	cis	Whole Blood	GTEx
rs35253817	GPR180	cis	Nerve Tibial	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	chr13:95254800-95258600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr13:95254800-95258600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr13:95254800-95259200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr13:95254800-95259200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr13:95254800-95259200	Weak transcription	Gastric	stomach
9	chr13:95254800-95263000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:95254800-95263800	Weak transcription	Left Ventricle	heart
11	chr13:95254800-95263800	Weak transcription	Pancreas	Pancrea
12	chr13:95254800-95263800	Weak transcription	Psoas Muscle	Psoas
13	chr13:95254800-95268200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr13:95254800-95272000	Weak transcription	Lung	lung
15	chr13:95254800-95275400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr13:95254800-95275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:95255000-95258600	Weak transcription	Placenta	Placenta
19	chr13:95255000-95259000	Weak transcription	Ovary	ovary
20	chr13:95255000-95259000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr13:95255000-95259000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr13:95255000-95259400	Weak transcription	Right Atrium	heart
23	chr13:95255000-95260200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr13:95255000-95260400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr13:95255000-95262800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr13:95255000-95262800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr13:95255000-95263200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr13:95255000-95263200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:95255000-95275400	Weak transcription	Aorta	Aorta
30	chr13:95255000-95275600	Weak transcription	Right Ventricle	heart
31	chr13:95255000-95276200	Weak transcription	HSMMtube	muscle
32	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
33	chr13:95255200-95258400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr13:95255200-95258800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr13:95255200-95259200	Weak transcription	Fetal Intestine Large	intestine
36	chr13:95255200-95259400	Weak transcription	Brain Germinal Matrix	brain
37	chr13:95255200-95262000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr13:95255200-95262800	Weak transcription	Fetal Kidney	kidney
39	chr13:95255200-95272200	Weak transcription	Colon Smooth Muscle	Colon
40	chr13:95255200-95276200	Weak transcription	Fetal Brain Female	brain
41	chr13:95255200-95278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
43	chr13:95255400-95259000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr13:95255400-95259200	Weak transcription	Stomach Mucosa	stomach
45	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr13:95255600-95258600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr13:95255600-95268000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
49	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
50	chr13:95255800-95258600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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