Variant report

Variant	rs17312912
Chromosome Location	chr12:12647608-12647609
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	chr12:12643142..12644757-chr12:12645381..12648713,3	MCF-7	breast:
2	chr12:12645901..12648123-chr12:12648969..12651125,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11830917	1.00[CHD][hapmap]
rs11831555	1.00[JPT][hapmap]
rs11833012	1.00[ASN][1000 genomes]
rs16908006	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16908222	1.00[CHD][hapmap]
rs17377986	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861674	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3741797	1.00[CHD][hapmap]
rs4529965	1.00[ASN][1000 genomes]
rs4763288	0.81[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763289	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763827	1.00[JPT][hapmap]
rs4763831	1.00[JPT][hapmap]
rs4763837	1.00[CHD][hapmap]
rs56015540	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488527	1.00[JPT][hapmap]
rs7133988	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7134787	1.00[JPT][hapmap]
rs714480	1.00[JPT][hapmap]
rs7306292	1.00[JPT][hapmap]
rs73063421	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73063424	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73063430	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73063437	1.00[ASN][1000 genomes]
rs7975061	1.00[JPT][hapmap]
rs7980390	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs888198	1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17312912	FGL2	trans	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
2	chr12:12622600-12653800	Weak transcription	Fetal Heart	heart
3	chr12:12626800-12653600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:12628800-12655800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:12630600-12661200	Weak transcription	NHEK	skin
6	chr12:12630800-12655800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:12630800-12658200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:12630800-12658400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:12630800-12659600	Weak transcription	Esophagus	oesophagus
10	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
11	chr12:12632800-12658200	Weak transcription	Ovary	ovary
12	chr12:12633000-12658600	Weak transcription	Fetal Kidney	kidney
13	chr12:12633400-12648800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
15	chr12:12634800-12658800	Weak transcription	HSMMtube	muscle
16	chr12:12636000-12653400	Weak transcription	Right Ventricle	heart
17	chr12:12636200-12655800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:12636800-12656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:12637200-12651600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:12639400-12648800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:12639400-12652800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:12639600-12648000	Weak transcription	Fetal Brain Female	brain
24	chr12:12639600-12655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:12639600-12659000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:12640000-12648800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:12640000-12648800	Weak transcription	Fetal Lung	lung
28	chr12:12640000-12652800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:12640000-12656600	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:12640000-12658000	Weak transcription	NHLF	lung
31	chr12:12640000-12658200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:12640000-12658200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:12640000-12658200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:12640200-12649200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:12640200-12649600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:12640200-12652200	Weak transcription	Placenta	Placenta
37	chr12:12640200-12652800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:12640200-12656600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:12640400-12659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:12640600-12649000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:12641200-12658200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:12641400-12652600	Weak transcription	A549	lung
43	chr12:12641600-12648800	Weak transcription	NH-A	brain
44	chr12:12641600-12649400	Weak transcription	Thymus	Thymus
45	chr12:12641600-12658800	Weak transcription	HUVEC	blood vessel
46	chr12:12641600-12663600	Weak transcription	Lung	lung
47	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:12641800-12649200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:12641800-12654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:12642200-12652400	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links