Variant report

Variant	rs2242405
Chromosome Location	chr16:75481771-75481772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75480575..75482180-chr16:75497109..75499874,2	K562	blood:
2	chr16:75466529..75469115-chr16:75481185..75484731,5	MCF-7	breast:
3	chr16:75474256..75476578-chr16:75479632..75482029,2	MCF-7	breast:
4	chr16:75467452..75469743-chr16:75480979..75483108,3	K562	blood:
5	chr16:75481686..75483472-chr16:75653624..75656494,2	K562	blood:
6	chr16:75480575..75485333-chr16:75494576..75499874,6	K562	blood:

Variant related genes	Relation type
ENSG00000153774	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000166822	Chromatin interaction
ENSG00000261717	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1017239	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.80[ASN][1000 genomes]
rs1030261	0.81[ASN][1000 genomes]
rs1030262	0.80[ASN][1000 genomes]
rs10514393	0.82[JPT][hapmap]
rs1074961	0.82[ASN][1000 genomes]
rs10781977	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap]
rs10871308	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs10871312	0.81[ASN][1000 genomes]
rs11149812	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs11149813	0.84[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs11149815	0.82[JPT][hapmap]
rs11644306	0.81[ASN][1000 genomes]
rs11645691	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11646418	0.81[ASN][1000 genomes]
rs11649638	0.81[ASN][1000 genomes]
rs12445813	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs12446903	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12927562	0.82[ASN][1000 genomes]
rs12928036	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12932952	0.82[ASN][1000 genomes]
rs12933281	0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12935329	0.82[ASN][1000 genomes]
rs1540	1.00[ASN][1000 genomes]
rs185052	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs185053	0.89[ASN][1000 genomes]
rs1862705	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2032926	0.80[ASN][1000 genomes]
rs2059257	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs2161684	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs247423	0.83[ASN][1000 genomes]
rs247424	0.82[ASN][1000 genomes]
rs247425	0.83[ASN][1000 genomes]
rs247427	0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs247431	0.84[ASN][1000 genomes]
rs247434	0.83[ASN][1000 genomes]
rs247436	0.84[ASN][1000 genomes]
rs247437	0.82[ASN][1000 genomes]
rs247438	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs247443	0.82[ASN][1000 genomes]
rs247447	0.90[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs247450	0.99[ASN][1000 genomes]
rs28558946	0.81[ASN][1000 genomes]
rs2865527	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35683383	0.81[ASN][1000 genomes]
rs37588	0.85[ASN][1000 genomes]
rs37589	0.85[ASN][1000 genomes]
rs37596	0.93[ASN][1000 genomes]
rs37599	0.96[ASN][1000 genomes]
rs37601	0.93[ASN][1000 genomes]
rs37602	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs37605	0.94[ASN][1000 genomes]
rs3784936	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3851735	0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3851736	0.81[ASN][1000 genomes]
rs40217	0.99[ASN][1000 genomes]
rs42472	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4536500	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs455407	0.84[ASN][1000 genomes]
rs467223	0.83[ASN][1000 genomes]
rs467780	0.83[ASN][1000 genomes]
rs468079	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4887827	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4887828	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887829	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4887830	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4888381	0.81[ASN][1000 genomes]
rs4888393	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4888394	0.82[ASN][1000 genomes]
rs4888395	0.82[ASN][1000 genomes]
rs4888396	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4888397	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4888398	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4888425	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4888427	0.81[ASN][1000 genomes]
rs4888430	0.80[CHB][hapmap]
rs4993971	0.91[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs59155720	0.81[ASN][1000 genomes]
rs59465235	0.82[ASN][1000 genomes]
rs7189407	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7199132	0.81[JPT][hapmap]
rs7201989	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7202284	0.95[JPT][hapmap]
rs7202596	0.81[ASN][1000 genomes]
rs7204984	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs766522	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8046184	0.82[ASN][1000 genomes]
rs8046416	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8046949	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8048677	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs8048816	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8049611	0.82[ASN][1000 genomes]
rs8050662	0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs8051611	0.81[ASN][1000 genomes]
rs8053632	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs8054586	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs8055609	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs889446	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs977986	0.94[ASN][1000 genomes]
rs9923834	0.94[ASN][1000 genomes]
rs9928232	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9933956	0.81[ASN][1000 genomes]
rs9934007	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9989421	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[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	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
2	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
3	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
4	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
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv521596	chr16:75466696-75486648	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2242405	TMEM170A	cis	Liver	GTEx
rs2242405	CFDP1	cis	parietal	SCAN
rs2242405	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs2242405	RFWD3	cis	cerebellum	SCAN
rs2242405	TMEM170	cis	multi-tissue	Pritchard
rs2242405	TMEM170A	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75468400-75482400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:75468400-75482600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:75468400-75489400	Weak transcription	Small Intestine	intestine
4	chr16:75468600-75482400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:75468600-75487800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:75468600-75489800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr16:75468800-75483000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr16:75468800-75483200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:75468800-75483600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr16:75468800-75483600	Weak transcription	Adipose Nuclei	Adipose
11	chr16:75468800-75483600	Weak transcription	Hela-S3	cervix
12	chr16:75468800-75483800	Weak transcription	HSMMtube	muscle
13	chr16:75468800-75484200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr16:75468800-75484400	Weak transcription	Brain Anterior Caudate	brain
15	chr16:75468800-75484400	Weak transcription	NHEK	skin
16	chr16:75468800-75484600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr16:75468800-75484600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr16:75468800-75484600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr16:75468800-75484800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr16:75468800-75484800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr16:75468800-75485400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr16:75468800-75486400	Weak transcription	Pancreas	Pancrea
23	chr16:75468800-75486400	Weak transcription	Right Atrium	heart
24	chr16:75468800-75486600	Weak transcription	HUVEC	blood vessel
25	chr16:75468800-75489200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr16:75468800-75493800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr16:75468800-75497000	Weak transcription	NHLF	lung
28	chr16:75469000-75483000	Weak transcription	Primary B cells from cord blood	blood
29	chr16:75469000-75483200	Weak transcription	Osteobl	bone
30	chr16:75469200-75481800	Weak transcription	A549	lung
31	chr16:75469400-75483400	Weak transcription	Fetal Brain Female	brain
32	chr16:75469400-75483600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr16:75469400-75484600	Weak transcription	Spleen	Spleen
34	chr16:75469400-75484800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr16:75469400-75484800	Weak transcription	Brain Angular Gyrus	brain
36	chr16:75469400-75484800	Weak transcription	Brain Hippocampus Middle	brain
37	chr16:75469400-75486600	Weak transcription	K562	blood
38	chr16:75469400-75491000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr16:75469400-75497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr16:75469400-75497400	Weak transcription	Psoas Muscle	Psoas
41	chr16:75470000-75482000	Weak transcription	Fetal Muscle Leg	muscle
42	chr16:75470000-75484600	Weak transcription	Right Ventricle	heart
43	chr16:75473600-75496000	Weak transcription	HMEC	breast
44	chr16:75474800-75483400	Weak transcription	Placenta	Placenta
45	chr16:75475000-75483200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr16:75476400-75482400	Weak transcription	Fetal Stomach	stomach
47	chr16:75476400-75483200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr16:75476400-75483600	Weak transcription	Fetal Kidney	kidney
49	chr16:75476400-75484600	Weak transcription	Thymus	Thymus
50	chr16:75476800-75485800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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