Variant report

Variant	rs2059257
Chromosome Location	chr16:75396376-75396377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 160 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs1011121	0.83[CHB][hapmap]
rs1017239	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10514393	0.87[CHB][hapmap]
rs10514396	0.83[CHB][hapmap]
rs1074961	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10781976	0.83[CHB][hapmap]
rs10781977	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10871307	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10871308	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1109342	0.83[CHB][hapmap]
rs11149812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11149813	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11149814	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11149815	0.81[CHB][hapmap]
rs11149816	0.90[ASN][1000 genomes]
rs11149831	0.83[CHB][hapmap]
rs11640018	0.83[CHB][hapmap]
rs11641532	0.82[CHB][hapmap]
rs11645691	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11646418	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11646677	0.83[CHB][hapmap]
rs12149063	0.83[CHB][hapmap]
rs12444589	0.83[CHB][hapmap]
rs12445188	0.89[ASN][1000 genomes]
rs12445211	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12445813	0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12446903	0.96[ASN][1000 genomes]
rs12449177	0.87[ASN][1000 genomes]
rs12922897	0.86[ASN][1000 genomes]
rs12932952	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12933281	0.82[CHB][hapmap]
rs12935329	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1364078	0.82[CHB][hapmap]
rs1540	0.86[EUR][1000 genomes]
rs1549306	0.83[CHB][hapmap]
rs1559339	0.83[CHB][hapmap]
rs17696696	0.83[CHB][hapmap]
rs17696749	0.83[CHB][hapmap]
rs185052	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1862705	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1895489	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1895490	0.83[CHB][hapmap]
rs2032926	0.92[ASN][1000 genomes]
rs2059256	0.82[CHB][hapmap]
rs2161648	0.83[CHB][hapmap]
rs2161684	0.82[CHB][hapmap]
rs2242405	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs247423	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247424	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247425	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247431	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247434	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247436	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247437	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247439	0.80[ASN][1000 genomes]
rs247443	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247447	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs247450	0.85[EUR][1000 genomes]
rs2865527	0.92[ASN][1000 genomes]
rs2865530	0.82[CHB][hapmap]
rs2865532	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2903033	0.82[CHB][hapmap]
rs3743606	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs37588	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37589	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37599	0.81[EUR][1000 genomes]
rs37602	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs3784936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784937	0.90[ASN][1000 genomes]
rs3844219	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851735	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851736	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851739	0.89[ASN][1000 genomes]
rs40217	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4146809	0.83[CHB][hapmap]
rs4146810	0.83[CHB][hapmap]
rs4243111	0.83[CHB][hapmap]
rs42472	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4536500	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs455407	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4638613	0.83[CHB][hapmap]
rs467223	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467780	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs468079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887812	0.80[EUR][1000 genomes]
rs4887813	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4887814	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887823	0.82[CHB][hapmap]
rs4887824	0.83[CHB][hapmap]
rs4887828	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs4888369	0.80[EUR][1000 genomes]
rs4888370	0.80[EUR][1000 genomes]
rs4888374	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888375	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888376	0.83[CHB][hapmap]
rs4888377	0.84[CHB][hapmap]
rs4888378	0.83[CHB][hapmap]
rs4888379	0.83[CHB][hapmap]
rs4888380	0.82[CHB][hapmap]
rs4888381	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4888383	0.83[CHB][hapmap]
rs4888388	0.83[CHB][hapmap]
rs4888393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888394	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888395	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888396	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs4888397	0.93[ASN][1000 genomes]
rs4888398	0.96[ASN][1000 genomes]
rs4888405	0.82[CHB][hapmap]
rs4888416	0.83[CHB][hapmap]
rs4888425	0.82[CHB][hapmap]
rs4888430	0.85[CHB][hapmap]
rs4993969	0.83[CHB][hapmap]
rs4993971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62062595	0.86[EUR][1000 genomes]
rs6564245	0.80[EUR][1000 genomes]
rs6564249	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6564256	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7187263	0.80[EUR][1000 genomes]
rs7187690	0.93[CEU][hapmap]
rs7188604	0.82[CHB][hapmap]
rs7189407	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7192155	0.92[ASN][1000 genomes]
rs7199132	0.82[CHB][hapmap]
rs7199680	0.88[ASN][1000 genomes]
rs7202083	0.83[EUR][1000 genomes]
rs7202284	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7203157	0.83[CHB][hapmap]
rs7204984	0.82[CHB][hapmap]
rs766521	0.83[CHB][hapmap]
rs766522	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs8046109	0.82[CHB][hapmap]
rs8046184	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8046416	0.86[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs8046949	0.96[ASN][1000 genomes]
rs8048677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8048816	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs8049611	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8050059	0.83[CHB][hapmap]
rs8050662	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8051611	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051785	0.90[ASN][1000 genomes]
rs8053632	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8054586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8055609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs889446	0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs9922008	0.85[CHB][hapmap]
rs9933956	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9934007	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs9989421	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	esv2762265	chr16:75368897-75415866	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
7	esv2422358	chr16:75381762-75456763	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2059257	TMEM170A	cis	parietal	SCAN
rs2059257	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr16:75354800-75413600	Weak transcription	Fetal Thymus	thymus
4	chr16:75358400-75421400	Weak transcription	K562	blood
5	chr16:75368600-75396600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr16:75368600-75411400	Weak transcription	GM12878-XiMat	blood
7	chr16:75368600-75412800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:75368800-75409800	Weak transcription	Thymus	Thymus
9	chr16:75368800-75413200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr16:75369200-75406000	Weak transcription	Dnd41	blood
11	chr16:75375200-75400000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:75375800-75408400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr16:75376600-75396600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr16:75376600-75410600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr16:75376600-75426800	Weak transcription	Brain Germinal Matrix	brain
16	chr16:75377000-75396400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr16:75377000-75396400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:75377000-75399200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr16:75377000-75399200	Weak transcription	Fetal Intestine Large	intestine
20	chr16:75377000-75411600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr16:75377000-75411800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr16:75377000-75424400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr16:75377000-75426400	Weak transcription	Gastric	stomach
24	chr16:75377200-75424000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr16:75377400-75426400	Weak transcription	Pancreas	Pancrea
26	chr16:75377600-75400000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr16:75377600-75405000	Weak transcription	Liver	Liver
28	chr16:75377600-75407600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr16:75377600-75410200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr16:75377600-75411800	Weak transcription	Left Ventricle	heart
31	chr16:75377800-75405000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr16:75378000-75410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr16:75378000-75411000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:75378400-75410400	Weak transcription	Fetal Kidney	kidney
35	chr16:75378600-75409600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:75380200-75397800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr16:75380200-75399400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr16:75380200-75411400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr16:75380200-75413200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr16:75381200-75403400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr16:75381400-75409400	Weak transcription	Placenta	Placenta
42	chr16:75383800-75399800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr16:75385400-75401000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr16:75385600-75404800	Weak transcription	Hela-S3	cervix
45	chr16:75385600-75405800	Weak transcription	NHDF-Ad	bronchial
46	chr16:75385800-75398200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr16:75385800-75399200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr16:75385800-75399200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr16:75385800-75404800	Weak transcription	Osteobl	bone
50	chr16:75385800-75405000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links