Variant report

Variant	rs12644709
Chromosome Location	chr4:55135580-55135581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10028020	0.81[EUR][1000 genomes]
rs1105825	0.82[EUR][1000 genomes]
rs12505491	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506290	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644749	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565669	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565670	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17084051	0.81[ASN][1000 genomes]
rs1800809	0.81[ASN][1000 genomes]
rs1800810	0.80[ASN][1000 genomes]
rs1800812	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1800813	0.81[ASN][1000 genomes]
rs2229307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307050	0.81[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs28374326	0.82[EUR][1000 genomes]
rs28489067	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28528897	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600756	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650939	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35597368	0.83[EUR][1000 genomes]
rs4358459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368668	0.80[ASN][1000 genomes]
rs4422471	0.81[ASN][1000 genomes]
rs4608869	0.80[ASN][1000 genomes]
rs4635872	0.80[ASN][1000 genomes]
rs4864857	0.81[ASN][1000 genomes]
rs4864858	0.80[ASN][1000 genomes]
rs4864859	0.81[ASN][1000 genomes]
rs4864860	0.81[ASN][1000 genomes]
rs4864861	0.81[ASN][1000 genomes]
rs4864862	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4864863	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4864864	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864865	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56145315	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58435984	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58727676	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61320297	0.81[ASN][1000 genomes]
rs6554163	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs67279506	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67388297	0.82[EUR][1000 genomes]
rs67432867	0.81[ASN][1000 genomes]
rs67600360	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836215	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6850748	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6855761	0.82[EUR][1000 genomes]
rs73252942	0.81[ASN][1000 genomes]
rs73252946	0.96[ASN][1000 genomes]
rs73252948	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673597	0.81[ASN][1000 genomes]
rs7673984	0.81[ASN][1000 genomes]
rs7677751	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7678144	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7679903	0.81[ASN][1000 genomes]
rs7681399	0.81[ASN][1000 genomes]
rs7682912	0.88[JPT][hapmap]
rs7686588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689569	0.81[ASN][1000 genomes]
rs7690503	0.81[ASN][1000 genomes]
rs7691129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698425	0.81[ASN][1000 genomes]
rs890203	0.81[ASN][1000 genomes]
rs9991165	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1004408	chr4:55124471-55179212	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv537099	chr4:55124471-55179212	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1001094	chr4:55131860-55189739	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55119000-55138600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:55119400-55148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:55121000-55147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:55121000-55153200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:55121200-55147200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:55122400-55142600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:55124400-55140400	Weak transcription	Placenta	Placenta
8	chr4:55124400-55147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:55124800-55138600	Weak transcription	NH-A	brain
10	chr4:55125400-55140600	Strong transcription	Ovary	ovary
11	chr4:55125800-55135800	Strong transcription	Fetal Lung	lung
12	chr4:55126400-55140800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:55127000-55138600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:55127200-55135600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:55127800-55140600	Weak transcription	Left Ventricle	heart
16	chr4:55129200-55139000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:55129200-55142400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:55129800-55136000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:55130000-55139000	Weak transcription	Esophagus	oesophagus
20	chr4:55130000-55139000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:55130200-55142800	Weak transcription	Gastric	stomach
22	chr4:55130200-55143000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:55130600-55142400	Weak transcription	Right Ventricle	heart
24	chr4:55131600-55148000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:55131800-55137200	Weak transcription	Spleen	Spleen
26	chr4:55132200-55142200	Weak transcription	Liver	Liver
27	chr4:55132400-55142800	Weak transcription	Adipose Nuclei	Adipose
28	chr4:55133000-55135600	Strong transcription	Aorta	Aorta
29	chr4:55133200-55143200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr4:55133400-55135600	Strong transcription	Fetal Muscle Leg	muscle
31	chr4:55133400-55135600	Genic enhancers	NHDF-Ad	bronchial
32	chr4:55133400-55135600	Genic enhancers	Osteobl	bone
33	chr4:55133400-55143000	Weak transcription	Colonic Mucosa	Colon
34	chr4:55133600-55135600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:55134000-55135600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:55134000-55141000	Weak transcription	Psoas Muscle	Psoas
37	chr4:55134200-55136600	Weak transcription	Fetal Kidney	kidney
38	chr4:55134200-55136800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:55134400-55135600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:55135000-55141400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:55135200-55135800	Strong transcription	NHLF	lung
42	chr4:55135200-55137200	Weak transcription	Fetal Intestine Large	intestine
43	chr4:55135200-55140000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:55135400-55136200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:55135400-55137000	Weak transcription	Fetal Stomach	stomach
46	chr4:55135400-55138200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:55135400-55138200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links