Variant report

Variant	rs329391
Chromosome Location	chr3:137782655-137782656
allele	A/G
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	chr3:137776797..137779428-chr3:137782269..137783995,2	MCF-7	breast:
5	chr12:90428505..90430564-chr3:137781378..137783907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158163	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1107422	0.89[ASN][1000 genomes]
rs11719358	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13100360	0.86[ASN][1000 genomes]
rs1444577	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1444578	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1545816	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1564496	0.81[ASN][1000 genomes]
rs17838821	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs179282	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2170309	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2246945	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2589259	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589260	0.85[EUR][1000 genomes]
rs2622697	0.81[ASN][1000 genomes]
rs2622704	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2622705	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2622706	0.94[ASN][1000 genomes]
rs2622707	0.94[ASN][1000 genomes]
rs2622709	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2622710	0.91[ASN][1000 genomes]
rs2622711	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2622714	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622715	0.88[ASN][1000 genomes]
rs2622716	0.88[ASN][1000 genomes]
rs2622717	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622718	0.88[ASN][1000 genomes]
rs2622719	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622720	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622724	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622725	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622726	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622727	0.86[ASN][1000 genomes]
rs2622728	0.86[ASN][1000 genomes]
rs2622729	0.86[ASN][1000 genomes]
rs2622730	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622745	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2622746	0.81[ASN][1000 genomes]
rs2724687	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2724693	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2724694	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724695	0.86[ASN][1000 genomes]
rs2724697	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2724698	0.94[ASN][1000 genomes]
rs2724699	0.94[ASN][1000 genomes]
rs2724700	0.94[ASN][1000 genomes]
rs2724701	0.94[ASN][1000 genomes]
rs2724702	0.94[ASN][1000 genomes]
rs2724703	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724704	0.94[ASN][1000 genomes]
rs2724705	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2724706	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2724707	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724708	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724713	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724716	0.86[ASN][1000 genomes]
rs2724717	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2724720	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724721	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724722	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724723	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724729	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs28480035	0.82[ASN][1000 genomes]
rs329381	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs329382	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs329383	0.85[ASN][1000 genomes]
rs329384	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs329385	0.86[ASN][1000 genomes]
rs329388	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329389	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365504	0.82[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367439	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs374045	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs382629	0.82[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs384828	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs389697	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs390729	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs405265	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs405517	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs405602	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs407009	0.94[ASN][1000 genomes]
rs419075	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs425938	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs436145	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs442800	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs445025	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs446644	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452195	0.94[ASN][1000 genomes]
rs453023	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4678403	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs618553	0.91[ASN][1000 genomes]
rs6809258	0.86[ASN][1000 genomes]
rs7613955	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7629243	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7639197	0.88[ASN][1000 genomes]
rs899983	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9814877	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834462	0.81[ASN][1000 genomes]
rs9834670	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9842918	0.83[ASN][1000 genomes]
rs9857908	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs9860229	0.81[ASN][1000 genomes]
rs996432	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv519971	chr3:137782655-137801213	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv522591	chr3:137782655-137801213	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137744400-137792000	Weak transcription	Fetal Kidney	kidney
2	chr3:137754400-137783000	Weak transcription	Stomach Mucosa	stomach
3	chr3:137763000-137797600	Weak transcription	Hela-S3	cervix
4	chr3:137766800-137783600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:137767000-137782800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:137767200-137791800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:137768200-137782800	Weak transcription	Esophagus	oesophagus
8	chr3:137768200-137787600	Weak transcription	A549	lung
9	chr3:137768600-137783600	Weak transcription	Pancreas	Pancrea
10	chr3:137769800-137785600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:137770200-137783600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:137770400-137783600	Weak transcription	Fetal Lung	lung
13	chr3:137772800-137792200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:137777800-137790000	Weak transcription	Brain Germinal Matrix	brain
15	chr3:137778200-137800600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:137778400-137787400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:137778600-137787600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:137778800-137800400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:137779200-137783000	Weak transcription	Colonic Mucosa	Colon
20	chr3:137779200-137792400	Strong transcription	Fetal Stomach	stomach
21	chr3:137779600-137782800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:137779600-137787600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:137779800-137787400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:137779800-137787600	Strong transcription	Adipose Nuclei	Adipose
25	chr3:137780000-137783800	Strong transcription	Spleen	Spleen
26	chr3:137780000-137784000	Strong transcription	Ovary	ovary
27	chr3:137780000-137785800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:137780000-137787200	Strong transcription	Aorta	Aorta
29	chr3:137780000-137792600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:137780000-137792600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:137780000-137797600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:137780000-137813400	Weak transcription	HUVEC	blood vessel
33	chr3:137780200-137783200	Strong transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:137780200-137786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:137780200-137787600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:137780400-137786600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:137780400-137787200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:137780400-137787400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:137780400-137787600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:137780400-137792400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:137780600-137784600	Weak transcription	GM12878-XiMat	blood
42	chr3:137780600-137786200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:137780600-137787200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:137780600-137787400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:137780600-137788000	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:137780600-137791600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:137780600-137811600	Weak transcription	Psoas Muscle	Psoas
48	chr3:137780800-137784200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:137780800-137800600	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:137781000-137784400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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