Variant report

Variant	rs11860980
Chromosome Location	chr16:75696506-75696507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75690994..75692895-chr16:75695592..75698180,2	MCF-7	breast:
2	chr16:75691958..75693608-chr16:75693696..75696714,3	MCF-7	breast:
3	chr16:75696333..75698717-chr16:75701380..75703728,2	K562	blood:

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

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

rs_ID	r²[population]
rs10468346	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1133766	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11546854	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640406	0.88[EUR][1000 genomes]
rs11640743	0.88[EUR][1000 genomes]
rs11641108	0.88[EUR][1000 genomes]
rs11646086	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11646574	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11648206	0.88[EUR][1000 genomes]
rs11649504	0.88[EUR][1000 genomes]
rs11649505	0.88[EUR][1000 genomes]
rs11649571	0.88[EUR][1000 genomes]
rs11862453	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864677	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942022	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942809	0.94[EUR][1000 genomes]
rs16942870	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs16943274	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16943285	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1865492	0.94[EUR][1000 genomes]
rs1991052	0.94[EUR][1000 genomes]
rs2233803	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2233805	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2233810	0.94[EUR][1000 genomes]
rs2242408	0.85[CEU][hapmap]
rs2453141	1.00[JPT][hapmap]
rs28571860	1.00[ASN][1000 genomes]
rs35135836	0.88[EUR][1000 genomes]
rs56892159	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58000098	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58657577	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58996069	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59624897	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59794444	0.89[EUR][1000 genomes]
rs60376290	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415088	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60545422	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60664312	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61588474	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62619985	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186790	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7193257	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7195089	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73613267	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73613272	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73615089	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8051771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053257	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs9989360	0.96[EUR][1000 genomes];1.00[ASN][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
rs11860980	KARS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75690600-75697000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:75691800-75697000	Weak transcription	Fetal Kidney	kidney
3	chr16:75691800-75697200	Weak transcription	Fetal Brain Male	brain
4	chr16:75692200-75697000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr16:75692200-75697000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr16:75692200-75697400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr16:75692200-75699400	Weak transcription	HSMMtube	muscle
8	chr16:75692400-75696600	Weak transcription	HepG2	liver
9	chr16:75692400-75697400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr16:75692400-75698600	Weak transcription	A549	lung
11	chr16:75692400-75704000	Weak transcription	Psoas Muscle	Psoas
12	chr16:75692800-75697000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr16:75692800-75697200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr16:75692800-75697200	Weak transcription	Osteobl	bone
15	chr16:75692800-75697400	Weak transcription	Colon Smooth Muscle	Colon
16	chr16:75692800-75697400	Weak transcription	Fetal Brain Female	brain
17	chr16:75693000-75696800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:75693000-75697000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr16:75693600-75697000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr16:75693800-75697200	Weak transcription	Fetal Intestine Large	intestine
21	chr16:75693800-75698600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:75693800-75723200	Weak transcription	Ovary	ovary
23	chr16:75694400-75705800	Weak transcription	Pancreas	Pancrea
24	chr16:75694600-75698000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr16:75694600-75698600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr16:75694800-75696600	Enhancers	Brain Substantia Nigra	brain
27	chr16:75694800-75697600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr16:75694800-75697800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr16:75695000-75696600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr16:75695000-75697400	Weak transcription	Fetal Intestine Small	intestine
31	chr16:75695000-75698800	Weak transcription	Fetal Muscle Leg	muscle
32	chr16:75695000-75702200	Weak transcription	Spleen	Spleen
33	chr16:75695200-75696800	Weak transcription	GM12878-XiMat	blood
34	chr16:75695200-75697600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr16:75695200-75699600	Weak transcription	Liver	Liver
36	chr16:75695400-75697000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr16:75695400-75697200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr16:75695400-75698600	Weak transcription	Fetal Thymus	thymus
39	chr16:75695600-75697200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr16:75695600-75697200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr16:75695600-75698800	Weak transcription	HSMM	muscle
42	chr16:75695600-75699200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr16:75695600-75704600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr16:75695600-75713200	Weak transcription	Right Atrium	heart
45	chr16:75695800-75697000	Weak transcription	HUVEC	blood vessel
46	chr16:75695800-75697400	Weak transcription	Primary T cells from cord blood	blood
47	chr16:75695800-75697400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr16:75695800-75699200	Weak transcription	Placenta	Placenta
49	chr16:75696000-75696600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr16:75696000-75697000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links