Variant report

Variant	rs1697757
Chromosome Location	chr12:75903560-75903561
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75901516..75903864-chr12:75903925..75905942,3	MCF-7	breast:
2	chr12:75895269..75897744-chr12:75903455..75905180,2	MCF-7	breast:
3	chr12:75897120..75901453-chr12:75903276..75905265,4	MCF-7	breast:
4	chr12:75722764..75725346-chr12:75903212..75905334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180881	Chromatin interaction
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1275478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1275481	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480004	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1604382	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1679378	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1697750	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1697752	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1697754	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1697756	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1795744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1824980	0.96[EUR][1000 genomes]
rs2173919	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2704766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2704767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4565938	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7966751	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7971504	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1697757	GLIPR1L2	cis	Artery Tibial	GTEx
rs1697757	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs1697757	RP11-585P4.5	cis	Artery Tibial	GTEx
rs1697757	GLIPR1L2	cis	lung	GTEx
rs1697757	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs1697757	GLIPR1L2	cis	Nerve Tibial	GTEx
rs1697757	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs1697757	GLIPR1L2	cis	Thyroid	GTEx
rs1697757	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs1697757	GLIPR1L2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
2	chr12:75880600-75903800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:75883800-75904800	Weak transcription	Esophagus	oesophagus
4	chr12:75888800-75903800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:75888800-75904200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:75891400-75903800	Weak transcription	Fetal Brain Male	brain
7	chr12:75892800-75904400	Weak transcription	Gastric	stomach
8	chr12:75893800-75903600	Weak transcription	Stomach Mucosa	stomach
9	chr12:75895400-75903800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:75895400-75903800	Weak transcription	Brain Substantia Nigra	brain
11	chr12:75895400-75904000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:75895400-75904200	Weak transcription	Right Ventricle	heart
13	chr12:75895400-75904400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:75895400-75904600	Weak transcription	Lung	lung
15	chr12:75895600-75904000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:75895800-75904800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:75896000-75903600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:75896200-75904000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:75896400-75903800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:75896400-75904000	Weak transcription	Fetal Heart	heart
21	chr12:75897000-75903600	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:75897000-75904000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:75897000-75904600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:75897200-75903800	Weak transcription	Brain Anterior Caudate	brain
25	chr12:75897400-75903800	Weak transcription	Brain Germinal Matrix	brain
26	chr12:75897400-75904000	Weak transcription	Aorta	Aorta
27	chr12:75897600-75903600	Weak transcription	Thymus	Thymus
28	chr12:75897600-75904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:75897600-75904800	Weak transcription	Spleen	Spleen
30	chr12:75897800-75904000	Weak transcription	Colonic Mucosa	Colon
31	chr12:75897800-75904600	Weak transcription	Left Ventricle	heart
32	chr12:75897800-75904800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:75898000-75903800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:75899600-75903800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:75899600-75903800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr12:75900000-75904400	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:75900200-75903800	Weak transcription	HSMMtube	muscle
38	chr12:75900400-75904600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr12:75900800-75903600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:75900800-75903800	Weak transcription	Fetal Lung	lung
41	chr12:75900800-75904400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:75900800-75904400	Weak transcription	Placenta	Placenta
43	chr12:75901600-75903600	Enhancers	NHLF	lung
44	chr12:75901600-75903800	Enhancers	Osteobl	bone
45	chr12:75901800-75903600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:75901800-75903800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:75901800-75903800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:75901800-75904200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:75902000-75903600	Enhancers	NHEK	skin
50	chr12:75902200-75903600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links