Variant report

Variant	rs1677154
Chromosome Location	chr12:31726869-31726870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31725804..31727316-chr12:31729688..31732236,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1012154	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1150945	0.81[AFR][1000 genomes]
rs1150950	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1150953	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1150954	0.85[AFR][1000 genomes]
rs1150955	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1259233	0.81[AFR][1000 genomes]
rs1259235	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1259353	0.81[AFR][1000 genomes]
rs1259356	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1259359	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259400	0.90[EUR][1000 genomes]
rs1259401	0.89[EUR][1000 genomes]
rs1259405	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1259422	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259423	0.89[EUR][1000 genomes]
rs1259427	0.82[EUR][1000 genomes]
rs1259430	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1259432	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1259437	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1259438	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1259441	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1262390	0.81[AFR][1000 genomes]
rs1271128	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1271663	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1272773	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1677173	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1677186	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1677187	0.80[EUR][1000 genomes]
rs1677189	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1716216	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2061761	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2568884	0.85[ASN][1000 genomes]
rs2568888	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2617190	0.85[ASN][1000 genomes]
rs2617200	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2682697	0.86[ASN][1000 genomes]
rs793146	0.86[ASN][1000 genomes]
rs793171	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs793174	0.81[AFR][1000 genomes]
rs793176	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs793180	0.86[ASN][1000 genomes]
rs793184	0.85[ASN][1000 genomes]
rs7974437	0.83[EUR][1000 genomes]
rs976874	0.81[AFR][1000 genomes];0.81[EUR][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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv52934	chr12:31721932-31731107	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31709200-31727600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:31711000-31727400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:31714200-31728600	Weak transcription	Psoas Muscle	Psoas
4	chr12:31719000-31731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:31720000-31727600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:31720000-31731400	Weak transcription	Brain Germinal Matrix	brain
7	chr12:31720200-31727400	Weak transcription	Brain Anterior Caudate	brain
8	chr12:31721600-31742400	Weak transcription	Aorta	Aorta
9	chr12:31722200-31731000	Weak transcription	HSMM	muscle
10	chr12:31722800-31727600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:31722800-31727600	Weak transcription	Adipose Nuclei	Adipose
12	chr12:31722800-31727800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:31722800-31730800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:31722800-31735200	Weak transcription	Spleen	Spleen
15	chr12:31723600-31728400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:31723800-31731400	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:31724000-31727600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:31724000-31728000	Weak transcription	Stomach Mucosa	stomach
19	chr12:31724000-31730800	Weak transcription	HSMMtube	muscle
20	chr12:31724200-31727200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:31724200-31727400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:31724200-31727400	Weak transcription	HUVEC	blood vessel
23	chr12:31724200-31727600	Weak transcription	Brain Substantia Nigra	brain
24	chr12:31724200-31727800	Weak transcription	Fetal Lung	lung
25	chr12:31724200-31727800	Weak transcription	NHLF	lung
26	chr12:31724200-31727800	Weak transcription	Osteobl	bone
27	chr12:31724200-31728600	Weak transcription	Fetal Intestine Small	intestine
28	chr12:31724200-31730800	Weak transcription	Pancreas	Pancrea
29	chr12:31724200-31730800	Weak transcription	Right Atrium	heart
30	chr12:31724200-31731000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:31724200-31731200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:31724200-31731400	Weak transcription	Fetal Kidney	kidney
33	chr12:31724200-31731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:31724400-31728000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:31724600-31727600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:31725000-31728600	Enhancers	Fetal Heart	heart
37	chr12:31725200-31727000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:31725200-31728200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:31725400-31727000	Enhancers	HepG2	liver
40	chr12:31725600-31728400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:31725800-31727200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr12:31725800-31727600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:31726000-31727200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:31726000-31727800	Enhancers	GM12878-XiMat	blood
45	chr12:31726200-31727000	Enhancers	Small Intestine	intestine
46	chr12:31726200-31727400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:31726200-31728800	Enhancers	A549	lung
48	chr12:31726200-31731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:31726400-31727000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr12:31726400-31727600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links