Variant report

Variant	rs6711707
Chromosome Location	chr2:36613556-36613557
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36612565..36614901-chr2:36618563..36620425,2	K562	blood:
2	chr2:36604191..36607049-chr2:36612212..36615757,3	K562	blood:

Variant related genes	Relation type
ENSG00000150938	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10178804	1.00[CHB][hapmap]
rs10186135	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10203010	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11124514	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11124515	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11124516	0.89[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1159133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12465297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12477836	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12994926	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13394052	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13407488	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2113632	0.82[EUR][1000 genomes]
rs2161904	0.82[EUR][1000 genomes]
rs2689711	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2888338	0.80[EUR][1000 genomes]
rs3755214	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3770913	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs3770924	0.85[CEU][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3770932	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770936	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3770946	0.92[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs3770947	0.92[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs3770963	0.82[EUR][1000 genomes]
rs4233914	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4670547	1.00[CHB][hapmap]
rs4670548	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4670554	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6721505	0.80[AMR][1000 genomes]
rs6755048	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs711255	1.00[JPT][hapmap]
rs7589917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848508	1.00[JPT][hapmap]
rs848513	1.00[JPT][hapmap]
rs848514	1.00[JPT][hapmap]
rs888075	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs888076	0.88[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs9308991	1.00[CHB][hapmap]
rs9308992	1.00[CHB][hapmap]
rs997602	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6711707	PRKD3	cis	lymphoblastoid	seeQTL
rs6711707	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36586200-36626600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:36604000-36614400	Genic enhancers	HUVEC	blood vessel
3	chr2:36604000-36617000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:36604400-36614000	Weak transcription	HSMMtube	muscle
5	chr2:36604400-36615000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:36604400-36615400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:36604400-36615600	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:36604400-36616400	Weak transcription	Gastric	stomach
9	chr2:36604400-36620600	Weak transcription	Fetal Brain Male	brain
10	chr2:36604400-36640400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:36604400-36640600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:36604600-36614800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:36604600-36617600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:36604600-36620800	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:36604800-36614400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:36607600-36620800	Weak transcription	Pancreas	Pancrea
17	chr2:36607800-36615800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:36608000-36614000	Weak transcription	Hela-S3	cervix
19	chr2:36608000-36614600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:36608600-36614000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:36608600-36614000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:36608600-36616200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:36608600-36616200	Weak transcription	Fetal Stomach	stomach
24	chr2:36608800-36613600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:36608800-36614200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:36608800-36615600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:36608800-36615600	Weak transcription	Fetal Kidney	kidney
28	chr2:36608800-36615600	Weak transcription	Fetal Lung	lung
29	chr2:36609000-36614000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:36609000-36614000	Genic enhancers	A549	lung
31	chr2:36609000-36615800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:36609200-36614000	Weak transcription	Spleen	Spleen
33	chr2:36609200-36619800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:36609400-36615600	Weak transcription	Fetal Intestine Small	intestine
35	chr2:36609400-36620000	Weak transcription	Lung	lung
36	chr2:36609600-36614000	Weak transcription	HMEC	breast
37	chr2:36609600-36614200	Weak transcription	Adipose Nuclei	Adipose
38	chr2:36609800-36614600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:36609800-36615600	Weak transcription	Ovary	ovary
40	chr2:36610000-36613800	Weak transcription	Aorta	Aorta
41	chr2:36610400-36617800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:36611200-36614800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:36611400-36614000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:36611600-36614600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:36611600-36615600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:36611600-36616800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:36611600-36619800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:36611600-36632400	Weak transcription	Esophagus	oesophagus
49	chr2:36611600-36635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:36611800-36613600	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links