Variant report

Variant	rs329388
Chromosome Location	chr3:137781923-137781924
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:137781336..137783358-chr3:137787171..137788980,2	MCF-7	breast:
2	chr3:137780995..137783087-chr3:137786062..137788578,2	MCF-7	breast:
3	chr3:137748327..137751099-chr3:137781297..137783702,2	MCF-7	breast:
4	chr12:90428505..90430564-chr3:137781378..137783907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158163	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1107422	0.87[ASN][1000 genomes]
rs11719358	0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13100360	0.84[ASN][1000 genomes]
rs1444577	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1444578	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1545816	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs17838821	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs179282	0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1825081	0.82[ASN][1000 genomes]
rs2170309	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2246945	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2589259	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589260	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2622704	0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2622705	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2622706	0.92[ASN][1000 genomes]
rs2622707	0.92[ASN][1000 genomes]
rs2622709	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2622710	0.89[ASN][1000 genomes]
rs2622711	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622714	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622715	0.86[ASN][1000 genomes]
rs2622716	0.86[ASN][1000 genomes]
rs2622717	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622718	0.86[ASN][1000 genomes]
rs2622719	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2622720	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2622724	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622725	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622726	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622727	0.84[ASN][1000 genomes]
rs2622728	0.84[ASN][1000 genomes]
rs2622729	0.84[ASN][1000 genomes]
rs2622730	0.88[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2622745	0.90[EUR][1000 genomes]
rs2724687	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2724693	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2724694	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2724695	0.84[ASN][1000 genomes]
rs2724697	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2724698	0.92[ASN][1000 genomes]
rs2724699	0.92[ASN][1000 genomes]
rs2724700	0.92[ASN][1000 genomes]
rs2724701	0.92[ASN][1000 genomes]
rs2724702	0.92[ASN][1000 genomes]
rs2724703	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724704	0.92[ASN][1000 genomes]
rs2724705	0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2724706	0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2724707	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724708	0.87[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724713	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724716	0.84[ASN][1000 genomes]
rs2724717	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2724720	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724721	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724722	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724723	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724729	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs28480035	0.80[ASN][1000 genomes]
rs329381	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs329382	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs329383	0.83[ASN][1000 genomes]
rs329384	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs329385	0.84[ASN][1000 genomes]
rs329389	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329390	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329391	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs365504	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs367439	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs374045	0.88[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs382629	0.88[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs384828	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs389697	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs390729	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs405265	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs405517	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs405602	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs407009	0.92[ASN][1000 genomes]
rs419075	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs425938	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs436145	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs442800	0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs445025	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs446644	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs452195	0.92[ASN][1000 genomes]
rs453023	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4678403	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs618553	0.89[ASN][1000 genomes]
rs6809258	0.84[ASN][1000 genomes]
rs7613955	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7629243	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7639197	0.86[ASN][1000 genomes]
rs899983	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9814877	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9834670	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842918	0.80[ASN][1000 genomes]
rs9857908	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs996432	0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription 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	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007857	chr3:137767454-137843106	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1008563	chr3:137776151-137801394	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1002136	chr3:137776151-137806500	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137744400-137792000	Weak transcription	Fetal Kidney	kidney
2	chr3:137750600-137782200	Weak transcription	Fetal Intestine Small	intestine
3	chr3:137754400-137783000	Weak transcription	Stomach Mucosa	stomach
4	chr3:137763000-137797600	Weak transcription	Hela-S3	cervix
5	chr3:137763400-137782600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:137766800-137783600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:137767000-137782800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:137767200-137791800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:137768200-137782800	Weak transcription	Esophagus	oesophagus
10	chr3:137768200-137787600	Weak transcription	A549	lung
11	chr3:137768400-137782200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:137768600-137782200	Weak transcription	Gastric	stomach
13	chr3:137768600-137783600	Weak transcription	Pancreas	Pancrea
14	chr3:137769800-137785600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:137770200-137783600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:137770400-137783600	Weak transcription	Fetal Lung	lung
17	chr3:137772800-137792200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:137777800-137790000	Weak transcription	Brain Germinal Matrix	brain
19	chr3:137778200-137782400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:137778200-137800600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:137778400-137787400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:137778600-137787600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:137778800-137800400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:137779000-137782000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:137779200-137782200	Weak transcription	Fetal Brain Female	brain
26	chr3:137779200-137783000	Weak transcription	Colonic Mucosa	Colon
27	chr3:137779200-137792400	Strong transcription	Fetal Stomach	stomach
28	chr3:137779600-137782200	Genic enhancers	Osteobl	bone
29	chr3:137779600-137782800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:137779600-137787600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:137779800-137782000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:137779800-137782400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:137779800-137787400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:137779800-137787600	Strong transcription	Adipose Nuclei	Adipose
35	chr3:137780000-137783800	Strong transcription	Spleen	Spleen
36	chr3:137780000-137784000	Strong transcription	Ovary	ovary
37	chr3:137780000-137785800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:137780000-137787200	Strong transcription	Aorta	Aorta
39	chr3:137780000-137792600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:137780000-137792600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr3:137780000-137797600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:137780000-137813400	Weak transcription	HUVEC	blood vessel
43	chr3:137780200-137782400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:137780200-137783200	Strong transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:137780200-137786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:137780200-137787600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:137780400-137782000	Genic enhancers	Right Ventricle	heart
48	chr3:137780400-137782400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:137780400-137786600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:137780400-137787200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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