Variant report

Variant	rs7997035
Chromosome Location	chr13:95247626-95247627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95247274..95249727-chr13:95251841..95255221,4	MCF-7	breast:
2	chr13:95246267..95250128-chr13:95251933..95256020,6	MCF-7	breast:
3	chr13:95242101..95243874-chr13:95245900..95247690,2	K562	blood:
4	chr13:95245952..95249992-chr13:95252491..95255739,5	K562	blood:
5	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: 13 )

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

rs_ID	r²[population]
rs1112370	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]
rs1408999	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1572935	0.86[GIH][hapmap];0.86[MEX][hapmap]
rs2275647	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2275648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298058	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs34350725	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34405130	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35253817	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35678857	0.99[ASN][1000 genomes]
rs3742107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3897473	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3897474	0.88[CEU][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4473052	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4489873	0.90[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4608209	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4773801	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492716	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492717	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492718	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7321239	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7330873	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7331814	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7339106	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7981788	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7991607	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7997333	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7998025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9301981	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301983	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516434	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9516437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516438	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516440	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516441	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9516443	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516445	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524547	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524553	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524554	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524555	0.81[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524556	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524557	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524559	0.81[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9556402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9556403	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9556405	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9561638	0.99[ASN][1000 genomes]
rs9561641	0.86[TSI][hapmap]
rs9561642	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590037	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7997035	GPR180	cis	Artery Tibial	GTEx
rs7997035	GPR180	cis	cerebellum	SCAN
rs7997035	GPR180	cis	parietal	SCAN
rs7997035	GPR180	cis	lung	GTEx
rs7997035	GPR180	cis	Adipose Subcutaneous	GTEx
rs7997035	GPR180	cis	Stomach	GTEx
rs7997035	GPC5	cis	parietal	SCAN
rs7997035	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs7997035	GPR180	cis	Esophagus Mucosa	GTEx
rs7997035	GPR180	cis	Nerve Tibial	GTEx
rs7997035	ZDHHC9	trans	parietal	SCAN
rs7997035	GPR180	cis	Muscle Skeletal	GTEx
rs7997035	GPR180	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95246200-95248000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr13:95246200-95248600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:95246400-95247800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr13:95246400-95247800	Flanking Active TSS	HMEC	breast
5	chr13:95246400-95248000	Flanking Active TSS	Liver	Liver
6	chr13:95246400-95248000	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr13:95246400-95248200	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr13:95246400-95248200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr13:95246400-95248200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr13:95246400-95248200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr13:95246400-95249000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr13:95246400-95249000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr13:95246600-95247800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr13:95246600-95247800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr13:95246600-95247800	Flanking Active TSS	Osteobl	bone
16	chr13:95246600-95248000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:95246600-95248000	Flanking Active TSS	HUVEC	blood vessel
18	chr13:95246800-95247800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr13:95246800-95247800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:95246800-95247800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr13:95246800-95247800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr13:95246800-95247800	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr13:95246800-95248000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr13:95246800-95248000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr13:95246800-95248000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr13:95246800-95248200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr13:95246800-95249000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr13:95247000-95247800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr13:95247000-95247800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr13:95247000-95247800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr13:95247000-95247800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr13:95247000-95247800	Flanking Active TSS	Fetal Thymus	thymus
33	chr13:95247000-95247800	Flanking Active TSS	Psoas Muscle	Psoas
34	chr13:95247000-95247800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr13:95247000-95248000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr13:95247000-95248000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr13:95247000-95248000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr13:95247000-95248000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr13:95247000-95248000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr13:95247000-95248200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr13:95247000-95248200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr13:95247000-95248200	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr13:95247000-95248800	Active TSS	GM12878-XiMat	blood
44	chr13:95247000-95249000	Active TSS	K562	blood
45	chr13:95247200-95247800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
46	chr13:95247200-95247800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:95247200-95247800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr13:95247200-95247800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr13:95247200-95247800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr13:95247200-95247800	Flanking Active TSS	Fetal Lung	lung

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