Variant report

Variant	rs7195089
Chromosome Location	chr16:75687061-75687062
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr16:75687061-75687093	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:75686643..75688597-chr16:75796082..75798583,2	MCF-7	breast:
2	chr16:75686117..75687728-chr16:75687810..75689374,2	MCF-7	breast:
3	chr16:75686566..75689385-chr16:75689669..75693543,4	K562	blood:

Variant related genes	Relation type
KARS	TF binding region
TERF2IP	TF binding region
ENSG00000166848	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10163345	0.83[EUR][1000 genomes]
rs10468346	1.00[JPT][hapmap]
rs1133766	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11546854	0.94[EUR][1000 genomes]
rs11640406	0.84[EUR][1000 genomes]
rs11640743	0.84[EUR][1000 genomes]
rs11641108	0.84[EUR][1000 genomes]
rs11646086	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11646574	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11648206	0.84[EUR][1000 genomes]
rs11649504	0.84[EUR][1000 genomes]
rs11649505	0.84[EUR][1000 genomes]
rs11649571	0.84[EUR][1000 genomes]
rs11860980	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11862453	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11864677	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11866252	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16941008	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16942022	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16942809	0.89[EUR][1000 genomes]
rs16942870	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs16943274	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16943285	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1865492	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1991052	0.89[EUR][1000 genomes]
rs2233803	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2233805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2233810	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242408	0.85[CEU][hapmap]
rs2453141	1.00[JPT][hapmap]
rs35135836	0.84[EUR][1000 genomes]
rs56892159	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58000098	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs58657577	0.94[EUR][1000 genomes]
rs58996069	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs59624897	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs59794444	0.94[EUR][1000 genomes]
rs60376290	0.98[EUR][1000 genomes]
rs60415088	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60545422	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60664312	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs61588474	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs62619985	0.94[EUR][1000 genomes]
rs6834	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs7186790	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7193257	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73613267	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73613272	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73615089	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8051771	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs8053257	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs9989360	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7195089	KARS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75683600-75689800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr16:75683800-75691800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:75683800-75692800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:75684200-75687400	Enhancers	Fetal Heart	heart
5	chr16:75684400-75687600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:75684400-75687800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr16:75684400-75688200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr16:75684400-75689000	Weak transcription	HSMMtube	muscle
9	chr16:75684400-75689400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr16:75684400-75689400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr16:75684400-75689800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:75684600-75687400	Weak transcription	Fetal Intestine Small	intestine
13	chr16:75684600-75688000	Weak transcription	Fetal Intestine Large	intestine
14	chr16:75684600-75695400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr16:75684800-75687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr16:75684800-75687400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr16:75684800-75687600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:75684800-75688000	Enhancers	Primary B cells from peripheral blood	blood
19	chr16:75684800-75688000	Enhancers	Brain Substantia Nigra	brain
20	chr16:75684800-75688200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr16:75684800-75688800	Weak transcription	Stomach Mucosa	stomach
22	chr16:75684800-75689200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:75684800-75689400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr16:75684800-75689800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr16:75685000-75688200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr16:75685000-75689400	Weak transcription	Fetal Kidney	kidney
27	chr16:75685400-75687600	Weak transcription	NH-A	brain
28	chr16:75685600-75687400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr16:75685600-75687400	Weak transcription	Fetal Thymus	thymus
30	chr16:75685600-75687400	Weak transcription	Left Ventricle	heart
31	chr16:75685600-75687400	Weak transcription	Lung	lung
32	chr16:75685600-75687400	Weak transcription	Thymus	Thymus
33	chr16:75685600-75687600	Weak transcription	Fetal Muscle Leg	muscle
34	chr16:75685600-75687600	Weak transcription	HSMM	muscle
35	chr16:75685600-75688000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr16:75685600-75688000	Enhancers	Duodenum Mucosa	Duodenum
37	chr16:75685600-75688000	Weak transcription	NHEK	skin
38	chr16:75685600-75688200	Weak transcription	Colonic Mucosa	Colon
39	chr16:75685600-75688400	Weak transcription	Esophagus	oesophagus
40	chr16:75685800-75688000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr16:75685800-75688000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr16:75685800-75688000	Enhancers	Colon Smooth Muscle	Colon
43	chr16:75685800-75688200	Weak transcription	A549	lung
44	chr16:75686000-75687400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr16:75686000-75687400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr16:75686000-75687600	Enhancers	Primary T cells from cord blood	blood
47	chr16:75686000-75688000	Enhancers	Brain Cingulate Gyrus	brain
48	chr16:75686000-75688000	Enhancers	Osteobl	bone
49	chr16:75686000-75689200	Weak transcription	Hela-S3	cervix
50	chr16:75686200-75687200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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