Variant report

Variant	rs6711891
Chromosome Location	chr2:73236669-73236670
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10166058	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10166220	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10167566	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs10174548	0.86[JPT][hapmap];0.84[YRI][hapmap]
rs10176939	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177159	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178854	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10178944	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10180720	0.87[CEU][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs10180995	0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap]
rs10189744	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10190861	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs10191665	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10192077	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10197305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209859	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1036512	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12233055	0.94[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13385994	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13388404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13390072	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13393567	0.81[EUR][1000 genomes]
rs13400920	0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap]
rs13400948	0.81[JPT][hapmap];0.90[MEX][hapmap];0.83[YRI][hapmap]
rs13403757	0.86[JPT][hapmap]
rs13403781	0.86[JPT][hapmap]
rs13416407	0.81[JPT][hapmap];0.88[YRI][hapmap]
rs13424057	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13427947	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1370383	0.87[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1430349	0.86[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs17008571	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17008611	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17008631	0.87[CEU][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1864488	0.86[JPT][hapmap];0.86[MEX][hapmap]
rs1992133	0.85[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs2421098	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3813222	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs3901273	0.86[JPT][hapmap];0.84[YRI][hapmap]
rs4144837	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4514897	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4527230	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55974516	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57536428	0.83[EUR][1000 genomes]
rs57937746	0.83[EUR][1000 genomes]
rs58993488	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61161134	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61650913	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62147721	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62147724	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62147732	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6546794	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6546796	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6546797	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6546800	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs6709938	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6710362	0.89[ASN][1000 genomes]
rs6710739	0.87[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs6710755	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs6713655	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717553	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6719333	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726940	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6727269	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6727919	0.81[CEU][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6729266	0.86[JPT][hapmap];0.90[MEX][hapmap]
rs6732369	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6736153	0.86[JPT][hapmap];0.90[MEX][hapmap]
rs6749237	0.90[JPT][hapmap]
rs6750069	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6754779	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6754858	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6757131	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6759243	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759733	0.94[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs727470	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs732178	0.94[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs732179	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732180	0.94[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7557173	0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[YRI][hapmap]
rs7559340	0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap]
rs7566904	0.87[CEU][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7570876	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7578757	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7579770	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7580216	0.94[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7597032	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602651	0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs891432	0.81[CEU][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs891433	0.81[CEU][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs893258	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs893259	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309467	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6711891	RAB11FIP5	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73194200-73248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:73207800-73263200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:73208000-73247600	Weak transcription	Primary B cells from cord blood	blood
4	chr2:73211000-73258400	Weak transcription	Colonic Mucosa	Colon
5	chr2:73212200-73247400	Weak transcription	HSMMtube	muscle
6	chr2:73212800-73238800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:73214000-73238400	Weak transcription	Fetal Lung	lung
8	chr2:73214200-73247800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:73214200-73286400	Weak transcription	Psoas Muscle	Psoas
10	chr2:73215800-73247400	Weak transcription	Thymus	Thymus
11	chr2:73215800-73263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:73216200-73248800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:73217400-73249000	Weak transcription	Ovary	ovary
14	chr2:73217800-73237400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:73220600-73249000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:73220600-73263200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:73221200-73263000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:73223200-73274600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:73224600-73261200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:73226200-73248800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:73227600-73249000	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:73227800-73240800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:73227800-73240800	Weak transcription	HSMM	muscle
24	chr2:73227800-73241000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:73227800-73241000	Weak transcription	NHLF	lung
26	chr2:73227800-73241400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:73227800-73248600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:73228000-73245800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:73228000-73248800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:73228400-73247400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:73228600-73248200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:73228800-73248600	Weak transcription	Placenta	Placenta
33	chr2:73230800-73245800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:73231000-73247400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:73232400-73236800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:73232600-73236800	Enhancers	Fetal Brain Male	brain
37	chr2:73233200-73270800	Weak transcription	Brain Germinal Matrix	brain
38	chr2:73233600-73240200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:73234000-73236800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:73234000-73237000	Strong transcription	HepG2	liver
41	chr2:73234400-73236800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr2:73234400-73237800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:73234600-73237600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:73234600-73237800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:73234800-73237000	Strong transcription	Lung	lung
46	chr2:73234800-73237800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:73235000-73237000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:73235000-73237000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:73235000-73237600	Strong transcription	Osteobl	bone
50	chr2:73235000-73239200	Weak transcription	HUVEC	blood vessel

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