Variant report

Variant	rs12746771
Chromosome Location	chr1:113584400-113584401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113421587..113424736-chr1:113583992..113587746,3	K562	blood:
2	chr1:113582748..113584867-chr1:113586962..113588673,2	K562	blood:
3	chr1:113491230..113494579-chr1:113582129..113585862,4	K562	blood:
4	chr1:113492748..113494579-chr1:113582129..113585122,2	K562	blood:
5	chr1:113497364..113499320-chr1:113583841..113586175,3	K562	blood:
6	chr1:113456052..113457873-chr1:113583219..113586071,2	K562	blood:
7	chr1:113496133..113500283-chr1:113583331..113586865,6	K562	blood:
8	chr1:113422357..113424436-chr1:113583945..113586627,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226419	Chromatin interaction
ENSG00000155380	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11102573	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102574	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102577	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11102578	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11102582	0.81[CEU][hapmap]
rs11584099	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584535	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11588345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590174	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12066274	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12128904	0.93[ASN][1000 genomes]
rs12129863	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140104	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1216766	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1216772	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216773	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216775	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216779	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216781	0.94[JPT][hapmap]
rs1216783	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216784	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1216785	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216790	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12184285	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12354228	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12740564	0.83[EUR][1000 genomes]
rs12744009	0.81[CEU][hapmap]
rs12745675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12754835	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1419136	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1544227	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1627925	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17014850	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030901	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030905	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030974	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs1728218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs1728219	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1728232	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1766862	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs1778024	0.94[JPT][hapmap]
rs1778025	0.94[JPT][hapmap]
rs1983929	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs2769259	0.90[ASN][1000 genomes]
rs2798687	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2798689	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2798691	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2798692	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34233065	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34565381	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3889656	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3951437	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4838975	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55894203	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61818171	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818172	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818173	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818174	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818176	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656041	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71659385	0.84[ASN][1000 genomes]
rs773430	0.87[ASN][1000 genomes]
rs773432	0.87[ASN][1000 genomes]
rs773433	0.87[ASN][1000 genomes]
rs773434	0.85[ASN][1000 genomes]
rs773435	0.86[ASN][1000 genomes]
rs773436	0.90[ASN][1000 genomes]
rs773439	0.88[ASN][1000 genomes]
rs773440	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9429508	0.84[EUR][1000 genomes]
rs9429509	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9787311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
12	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113572600-113584600	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:113578000-113584800	Weak transcription	Hela-S3	cervix
3	chr1:113579800-113584400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:113579800-113584400	Weak transcription	Osteobl	bone
5	chr1:113579800-113584600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:113579800-113584600	Weak transcription	NHDF-Ad	bronchial
7	chr1:113579800-113584800	Weak transcription	Psoas Muscle	Psoas
8	chr1:113580000-113584400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:113580000-113584400	Weak transcription	Fetal Thymus	thymus
10	chr1:113580200-113589200	Weak transcription	Right Atrium	heart
11	chr1:113582000-113585000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:113582200-113584600	Enhancers	HUVEC	blood vessel
13	chr1:113582600-113584400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:113582600-113586000	Enhancers	Fetal Heart	heart
15	chr1:113582600-113586400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:113582600-113587400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:113582800-113585600	Enhancers	Brain Substantia Nigra	brain
18	chr1:113582800-113587600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:113583000-113584400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:113583000-113584600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:113583000-113585800	Enhancers	Stomach Mucosa	stomach
22	chr1:113583200-113584400	Weak transcription	Fetal Intestine Large	intestine
23	chr1:113583200-113584400	Weak transcription	Placenta	Placenta
24	chr1:113583200-113584400	Weak transcription	HepG2	liver
25	chr1:113583200-113584800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:113583200-113585000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:113583200-113585000	Enhancers	K562	blood
28	chr1:113583400-113584600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:113583400-113584800	Weak transcription	Small Intestine	intestine
30	chr1:113583400-113586600	Enhancers	NHEK	skin
31	chr1:113583600-113584600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:113583600-113584600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:113583600-113584600	Enhancers	GM12878-XiMat	blood
34	chr1:113583600-113584800	Enhancers	H9 Cell Line	embryonic stem cell
35	chr1:113583600-113584800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:113583600-113585000	Enhancers	Brain Cingulate Gyrus	brain
37	chr1:113583800-113584800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr1:113583800-113584800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:113583800-113586600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:113583800-113586600	Enhancers	Brain Anterior Caudate	brain
41	chr1:113584000-113584400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr1:113584000-113585000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:113584000-113586600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:113584000-113586600	Enhancers	HSMM	muscle
45	chr1:113584000-113586800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:113584000-113586800	Enhancers	Fetal Intestine Small	intestine
47	chr1:113584200-113584400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:113584200-113584600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr1:113584200-113584600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:113584200-113584600	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links