Variant report

Variant	rs2704767
Chromosome Location	chr12:75903191-75903192
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	chr12:75901516..75903864-chr12:75903925..75905942,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10879928	0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap]
rs11180481	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1275474	0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[LWK][hapmap]
rs1275478	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1275480	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1275481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1480004	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1604382	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1679378	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1697750	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1697752	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1697754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1697756	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1697757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1795744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1824980	0.96[EUR][1000 genomes]
rs2173919	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2704766	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4391857	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4565938	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7966751	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7971504	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2704767	GLIPR1L2	cis	Nerve Tibial	GTEx
rs2704767	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2704767	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs2704767	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs2704767	GLIPR1	cis	normal skin	skin_eQTL
rs2704767	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs2704767	GLIPR1L2	cis	parietal	SCAN
rs2704767	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs2704767	RP11-585P4.5	cis	Artery Tibial	GTEx
rs2704767	GLIPR1	cis	cerebellum	SCAN
rs2704767	GLIPR1L2	cis	Artery Tibial	GTEx
rs2704767	GLIPR1L2	cis	lung	GTEx
rs2704767	GLIPR1L2	cis	Thyroid	GTEx
rs2704767	GLIPR1L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75875600-75903400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
3	chr12:75876200-75903400	Weak transcription	Fetal Stomach	stomach
4	chr12:75880600-75903800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:75882600-75903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:75883800-75904800	Weak transcription	Esophagus	oesophagus
7	chr12:75886200-75903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:75888600-75903200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:75888800-75903800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:75888800-75904200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:75890600-75903200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:75891400-75903800	Weak transcription	Fetal Brain Male	brain
13	chr12:75892800-75904400	Weak transcription	Gastric	stomach
14	chr12:75893800-75903600	Weak transcription	Stomach Mucosa	stomach
15	chr12:75895400-75903800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:75895400-75903800	Weak transcription	Brain Substantia Nigra	brain
17	chr12:75895400-75904000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:75895400-75904200	Weak transcription	Right Ventricle	heart
19	chr12:75895400-75904400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:75895400-75904600	Weak transcription	Lung	lung
21	chr12:75895600-75904000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:75895800-75904800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:75896000-75903600	Weak transcription	Brain Angular Gyrus	brain
24	chr12:75896200-75904000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:75896400-75903800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:75896400-75904000	Weak transcription	Fetal Heart	heart
27	chr12:75897000-75903400	Weak transcription	Fetal Brain Female	brain
28	chr12:75897000-75903600	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:75897000-75904000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:75897000-75904600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:75897200-75903800	Weak transcription	Brain Anterior Caudate	brain
32	chr12:75897400-75903400	Weak transcription	Psoas Muscle	Psoas
33	chr12:75897400-75903800	Weak transcription	Brain Germinal Matrix	brain
34	chr12:75897400-75904000	Weak transcription	Aorta	Aorta
35	chr12:75897600-75903200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:75897600-75903600	Weak transcription	Thymus	Thymus
37	chr12:75897600-75904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:75897600-75904800	Weak transcription	Spleen	Spleen
39	chr12:75897800-75904000	Weak transcription	Colonic Mucosa	Colon
40	chr12:75897800-75904600	Weak transcription	Left Ventricle	heart
41	chr12:75897800-75904800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:75898000-75903400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:75898000-75903800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:75898800-75903400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:75899600-75903800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:75899600-75903800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:75899800-75903200	Strong transcription	HSMM	muscle
48	chr12:75900000-75903400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:75900000-75904400	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:75900200-75903200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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