Variant report

Variant	rs10167116
Chromosome Location	chr2:231071861-231071862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10168057	0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10174493	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10183659	1.00[AMR][1000 genomes]
rs10187268	1.00[AMR][1000 genomes]
rs13385973	0.98[AFR][1000 genomes]
rs13390432	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13392074	1.00[AMR][1000 genomes]
rs13397352	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28733458	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10167116	CKLF	trans	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231035400-231077000	Weak transcription	HepG2	liver
2	chr2:231036800-231073600	Weak transcription	HMEC	breast
3	chr2:231059000-231082800	Weak transcription	Stomach Mucosa	stomach
4	chr2:231062200-231081600	Strong transcription	Liver	Liver
5	chr2:231062400-231074000	Strong transcription	Primary T cells from cord blood	blood
6	chr2:231062400-231081600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:231062600-231073200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:231062600-231073600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:231062600-231079200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr2:231062600-231080600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:231062600-231081400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:231062600-231081400	Strong transcription	Adipose Nuclei	Adipose
13	chr2:231062600-231081400	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:231062600-231081400	Strong transcription	Fetal Thymus	thymus
15	chr2:231062600-231081600	Strong transcription	Fetal Lung	lung
16	chr2:231062600-231081600	Strong transcription	Placenta	Placenta
17	chr2:231062600-231081600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:231062600-231081600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:231062600-231081800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:231062600-231082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:231062600-231082400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:231062600-231084200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:231062800-231080600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr2:231062800-231081000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:231063000-231073400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:231063000-231077000	Weak transcription	Psoas Muscle	Psoas
27	chr2:231063000-231080200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:231063000-231084000	Weak transcription	Hela-S3	cervix
29	chr2:231063200-231073000	Strong transcription	Dnd41	blood
30	chr2:231063200-231073200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:231063200-231073800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:231063200-231074400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:231063200-231074400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:231063200-231075800	Weak transcription	Colonic Mucosa	Colon
35	chr2:231063200-231081200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:231063200-231084000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:231063400-231082200	Strong transcription	Fetal Muscle Leg	muscle
38	chr2:231063600-231072600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:231063800-231072000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:231064800-231084000	Weak transcription	Fetal Heart	heart
41	chr2:231065000-231081000	Strong transcription	Fetal Intestine Large	intestine
42	chr2:231065000-231081400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:231066200-231083200	Weak transcription	HUVEC	blood vessel
44	chr2:231066200-231084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:231066400-231081600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:231066800-231074800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:231067000-231074400	Genic enhancers	Primary B cells from cord blood	blood
48	chr2:231067000-231074600	Strong transcription	Thymus	Thymus
49	chr2:231067000-231076600	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr2:231067000-231077400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links