Variant report

Variant	rs3889656
Chromosome Location	chr1:113585261-113585262
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113421587..113424736-chr1:113583992..113587746,3	K562	blood:
2	chr1:113351549..113352456-chr1:113584930..113585890,3	K562	blood:
3	chr1:113420602..113421810-chr1:113584981..113585927,5	K562	blood:
4	chr1:113498269..113498996-chr1:113584965..113585589,2	MCF-7	breast:
5	chr1:113491230..113494579-chr1:113582129..113585862,4	K562	blood:
6	chr1:113259009..113259528-chr1:113585120..113585818,2	K562	blood:
7	chr1:113497364..113499320-chr1:113583841..113586175,3	K562	blood:
8	chr1:113585139..113585958-chr1:113615102..113615803,3	K562	blood:
9	chr1:113261144..113261746-chr1:113584996..113585576,2	K562	blood:
10	chr1:113423270..113424538-chr1:113584948..113585944,13	K562	blood:
11	chr1:113582365..113584393-chr1:113584924..113587944,3	K562	blood:
12	chr1:113477969..113479659-chr1:113584664..113586231,2	K562	blood:
13	chr1:113585160..113585865-chr1:113615154..113616308,3	MCF-7	breast:
14	chr1:113423306..113424369-chr1:113584838..113585867,15	MCF-7	breast:
15	chr1:113456052..113457873-chr1:113583219..113586071,2	K562	blood:
16	chr1:113351564..113352512-chr1:113584963..113585860,4	MCF-7	breast:
17	chr1:113496133..113500283-chr1:113583331..113586865,6	K562	blood:
18	chr1:113584615..113586115-chr20:55844916..55846959,2	MCF-7	breast:
19	chr1:113498071..113501633-chr1:113584474..113587906,3	MCF-7	breast:
20	chr1:113351443..113352326-chr1:113584981..113585924,5	MCF-7	breast:
21	chr1:113422357..113424436-chr1:113583945..113586627,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198799	Chromatin interaction
ENSG00000238198	Chromatin interaction
ENSG00000226419	Chromatin interaction
ENSG00000155380	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11102562	0.82[CEU][hapmap]
rs11102573	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102574	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102575	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102576	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102577	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11102578	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11102582	0.82[CEU][hapmap]
rs11584099	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584535	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11588345	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590170	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590174	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12028967	0.82[CEU][hapmap]
rs12066274	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12128904	0.93[ASN][1000 genomes]
rs12129863	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140104	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1216766	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1216772	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216773	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216775	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216779	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216781	0.87[JPT][hapmap]
rs1216783	0.83[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216784	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1216785	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216790	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1216801	0.82[CEU][hapmap]
rs12184285	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12354228	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12740564	0.83[EUR][1000 genomes]
rs12744009	0.83[CEU][hapmap]
rs12745675	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12746771	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]
rs12754835	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1419136	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1539625	0.82[CEU][hapmap]
rs1544227	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1627925	0.94[ASN][1000 genomes]
rs17014850	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030901	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030905	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030974	0.83[CEU][hapmap]
rs1728218	0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1728219	0.94[ASN][1000 genomes]
rs1728232	0.93[ASN][1000 genomes]
rs1766862	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs1778024	0.87[JPT][hapmap]
rs1778025	0.87[JPT][hapmap]
rs1983929	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2769259	0.90[ASN][1000 genomes]
rs2798687	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2798689	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2798691	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2798692	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34233065	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34565381	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3951437	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4301628	0.86[CEU][hapmap]
rs4838975	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4839273	0.86[CEU][hapmap]
rs55894203	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs61818171	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818172	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818173	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818174	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818176	0.93[AFR][1000 genomes];0.94[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];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[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	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9429508	0.85[EUR][1000 genomes]
rs9429509	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9429713	0.80[EUR][1000 genomes]
rs9787311	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113580200-113589200	Weak transcription	Right Atrium	heart
2	chr1:113582600-113586000	Enhancers	Fetal Heart	heart
3	chr1:113582600-113586400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:113582600-113587400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:113582800-113585600	Enhancers	Brain Substantia Nigra	brain
6	chr1:113582800-113587600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:113583000-113585800	Enhancers	Stomach Mucosa	stomach
8	chr1:113583400-113586600	Enhancers	NHEK	skin
9	chr1:113583800-113586600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:113583800-113586600	Enhancers	Brain Anterior Caudate	brain
11	chr1:113584000-113586600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:113584000-113586600	Enhancers	HSMM	muscle
13	chr1:113584000-113586800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:113584000-113586800	Enhancers	Fetal Intestine Small	intestine
15	chr1:113584200-113585400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:113584200-113585800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:113584200-113586200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:113584200-113586400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:113584200-113586600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:113584200-113586800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:113584200-113586800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:113584400-113585400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:113584400-113585400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:113584400-113585400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr1:113584400-113585600	Enhancers	Brain Germinal Matrix	brain
26	chr1:113584400-113585600	Enhancers	Fetal Stomach	stomach
27	chr1:113584400-113585800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:113584400-113585800	Enhancers	HSMMtube	muscle
29	chr1:113584400-113586000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:113584400-113586000	Enhancers	Dnd41	blood
31	chr1:113584400-113586400	Enhancers	Osteobl	bone
32	chr1:113584400-113586600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:113584400-113586600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:113584400-113586600	Enhancers	Fetal Muscle Leg	muscle
35	chr1:113584400-113586600	Enhancers	Placenta	Placenta
36	chr1:113584400-113586800	Enhancers	Fetal Intestine Large	intestine
37	chr1:113584400-113586800	Enhancers	Fetal Kidney	kidney
38	chr1:113584400-113587000	Enhancers	Fetal Thymus	thymus
39	chr1:113584600-113585400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr1:113584600-113585400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:113584600-113585400	Enhancers	Fetal Lung	lung
42	chr1:113584600-113585600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:113584600-113585600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:113584600-113585800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:113584600-113585800	Enhancers	Colon Smooth Muscle	Colon
46	chr1:113584600-113585800	Flanking Active TSS	GM12878-XiMat	blood
47	chr1:113584600-113585800	Flanking Active TSS	HUVEC	blood vessel
48	chr1:113584600-113585800	Flanking Active TSS	NH-A	brain
49	chr1:113584600-113585800	Enhancers	NHLF	lung
50	chr1:113584600-113586000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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