Variant report

Variant	rs1112370
Chromosome Location	chr13:95246440-95246441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95246267..95250128-chr13:95251933..95256020,6	MCF-7	breast:
2	chr13:95242101..95243874-chr13:95245900..95247690,2	K562	blood:
3	chr13:95245952..95249992-chr13:95252491..95255739,5	K562	blood:
4	chr13:95242026..95244794-chr13:95245664..95248411,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152749	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1408999	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1572935	0.91[GIH][hapmap]
rs2275647	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2275648	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298058	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs34350725	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405130	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35253817	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35678857	0.99[ASN][1000 genomes]
rs3742107	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3897473	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3897474	0.89[ASW][hapmap];0.84[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4473052	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4489873	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs4608209	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773801	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492716	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492717	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492718	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321239	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330873	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331814	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7339106	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981788	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7991607	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997035	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7997333	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998025	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9301979	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301981	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301983	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516434	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9516437	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9516438	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516440	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516441	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516443	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516445	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524545	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524547	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524548	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524549	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524550	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524551	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524553	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524554	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524555	0.95[GIH][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9524556	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9524557	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9524559	0.95[GIH][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9556402	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9556403	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9556405	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9561638	1.00[ASN][1000 genomes]
rs9561641	0.86[TSI][hapmap]
rs9561642	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590037	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	esv3521585	chr13:95244823-95249508	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
5	esv3497281	chr13:95244835-95249503	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
6	esv3497282	chr13:95244837-95249504	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
7	esv3521596	chr13:95244837-95249504	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1112370	ITR	cis	multi-tissue	Pritchard
rs1112370	GPR180	cis	Esophagus Mucosa	GTEx
rs1112370	GPR180	cis	Stomach	GTEx
rs1112370	GPR180	cis	Adipose Subcutaneous	GTEx
rs1112370	GPR180	cis	Artery Tibial	GTEx
rs1112370	GPR180	cis	Muscle Skeletal	GTEx
rs1112370	GPR180	cis	Whole Blood	GTEx
rs1112370	GPR180	cis	lung	GTEx
rs1112370	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs1112370	GPR180	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95222000-95247200	Weak transcription	Fetal Brain Male	brain
2	chr13:95225000-95247400	Weak transcription	Fetal Brain Female	brain
3	chr13:95226800-95246800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr13:95233000-95246600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr13:95233200-95246600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:95233200-95247000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr13:95233400-95247600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr13:95234400-95246800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:95234400-95246800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr13:95234400-95247000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:95234600-95247200	Weak transcription	Lung	lung
12	chr13:95235000-95246800	Weak transcription	Spleen	Spleen
13	chr13:95235200-95246600	Weak transcription	Psoas Muscle	Psoas
14	chr13:95235200-95246800	Weak transcription	Right Ventricle	heart
15	chr13:95235200-95247000	Weak transcription	Ovary	ovary
16	chr13:95235200-95247400	Weak transcription	Gastric	stomach
17	chr13:95235600-95246800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:95235600-95246800	Weak transcription	Pancreas	Pancrea
19	chr13:95235600-95247000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr13:95235600-95247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:95235600-95247400	Weak transcription	Aorta	Aorta
22	chr13:95235600-95247400	Weak transcription	HSMMtube	muscle
23	chr13:95236600-95246600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr13:95237600-95246600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr13:95237600-95246800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr13:95238000-95246800	Weak transcription	Left Ventricle	heart
27	chr13:95243600-95246600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr13:95243800-95246800	Weak transcription	Fetal Muscle Leg	muscle
29	chr13:95244400-95246800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr13:95244600-95246800	Weak transcription	Colonic Mucosa	Colon
31	chr13:95244600-95246800	Weak transcription	Fetal Kidney	kidney
32	chr13:95244600-95246800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:95244600-95246800	Weak transcription	NHDF-Ad	bronchial
34	chr13:95244600-95247000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr13:95244600-95247400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr13:95244800-95246600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr13:95244800-95246600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr13:95244800-95246800	Weak transcription	HSMM	muscle
39	chr13:95244800-95247000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr13:95245000-95246600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr13:95245000-95246600	Weak transcription	Fetal Thymus	thymus
42	chr13:95245000-95246600	Weak transcription	Small Intestine	intestine
43	chr13:95245000-95246800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr13:95245000-95246800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr13:95245000-95247000	Weak transcription	Placenta	Placenta
46	chr13:95245000-95247400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr13:95245200-95246600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr13:95245400-95246600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr13:95245400-95246600	Weak transcription	Fetal Intestine Large	intestine
50	chr13:95245400-95246600	Weak transcription	Fetal Intestine Small	intestine

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