Variant report

Variant	rs11864677
Chromosome Location	chr16:75696292-75696293
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75690994..75692895-chr16:75695592..75698180,2	MCF-7	breast:
2	chr16:75691958..75693608-chr16:75693696..75696714,3	MCF-7	breast:

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];0.92[EUR][1000 genomes]
rs11546854	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640406	0.92[EUR][1000 genomes]
rs11640743	0.92[EUR][1000 genomes]
rs11641108	0.92[EUR][1000 genomes]
rs11646086	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs11646574	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11648206	0.92[EUR][1000 genomes]
rs11649504	0.92[EUR][1000 genomes]
rs11649505	0.92[EUR][1000 genomes]
rs11649571	0.92[EUR][1000 genomes]
rs11860980	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862453	0.91[AFR][1000 genomes];1.00[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942022	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942809	0.90[EUR][1000 genomes]
rs16942870	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs16943274	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16943285	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1865492	0.90[EUR][1000 genomes]
rs1991052	0.90[EUR][1000 genomes]
rs2233803	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2233805	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2233810	0.90[EUR][1000 genomes]
rs2242408	0.85[CEU][hapmap]
rs2453141	1.00[JPT][hapmap]
rs28571860	1.00[ASN][1000 genomes]
rs35135836	0.92[EUR][1000 genomes]
rs56892159	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58000098	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58657577	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58996069	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59624897	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59794444	0.86[EUR][1000 genomes]
rs60376290	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415088	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60545422	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60664312	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61588474	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62619985	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7193257	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7195089	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73613267	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73613272	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73615089	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8051771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053257	0.85[CEU][hapmap]
rs9989360	0.92[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
rs11864677	KARS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75687600-75696400	Strong transcription	Primary B cells from cord blood	blood
2	chr16:75687600-75696400	Strong transcription	Fetal Stomach	stomach
3	chr16:75688600-75696400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr16:75690600-75697000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr16:75691800-75697000	Weak transcription	Fetal Kidney	kidney
6	chr16:75691800-75697200	Weak transcription	Fetal Brain Male	brain
7	chr16:75692200-75697000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr16:75692200-75697000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr16:75692200-75697400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr16:75692200-75699400	Weak transcription	HSMMtube	muscle
11	chr16:75692400-75696400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:75692400-75696600	Weak transcription	HepG2	liver
13	chr16:75692400-75697400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr16:75692400-75698600	Weak transcription	A549	lung
15	chr16:75692400-75704000	Weak transcription	Psoas Muscle	Psoas
16	chr16:75692800-75697000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr16:75692800-75697200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr16:75692800-75697200	Weak transcription	Osteobl	bone
19	chr16:75692800-75697400	Weak transcription	Colon Smooth Muscle	Colon
20	chr16:75692800-75697400	Weak transcription	Fetal Brain Female	brain
21	chr16:75693000-75696400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr16:75693000-75696800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:75693000-75697000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr16:75693600-75697000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr16:75693800-75697200	Weak transcription	Fetal Intestine Large	intestine
26	chr16:75693800-75698600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:75693800-75723200	Weak transcription	Ovary	ovary
28	chr16:75694400-75705800	Weak transcription	Pancreas	Pancrea
29	chr16:75694600-75696400	Enhancers	Adipose Nuclei	Adipose
30	chr16:75694600-75698000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr16:75694600-75698600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr16:75694800-75696400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr16:75694800-75696600	Enhancers	Brain Substantia Nigra	brain
34	chr16:75694800-75697600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr16:75694800-75697800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr16:75695000-75696400	Enhancers	Brain Hippocampus Middle	brain
37	chr16:75695000-75696600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr16:75695000-75697400	Weak transcription	Fetal Intestine Small	intestine
39	chr16:75695000-75698800	Weak transcription	Fetal Muscle Leg	muscle
40	chr16:75695000-75702200	Weak transcription	Spleen	Spleen
41	chr16:75695200-75696400	Strong transcription	Aorta	Aorta
42	chr16:75695200-75696800	Weak transcription	GM12878-XiMat	blood
43	chr16:75695200-75697600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr16:75695200-75699600	Weak transcription	Liver	Liver
45	chr16:75695400-75697000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr16:75695400-75697200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr16:75695400-75698600	Weak transcription	Fetal Thymus	thymus
48	chr16:75695600-75697200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr16:75695600-75697200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr16:75695600-75698800	Weak transcription	HSMM	muscle

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