Variant report

Variant	rs340647
Chromosome Location	chr4:87942234-87942235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87940559..87943450-chr4:87945338..87947892,3	K562	blood:
2	chr4:87926004..87930134-chr4:87942000..87950091,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10003332	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10008600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10022960	0.89[ASN][1000 genomes]
rs11931688	1.00[CEU][hapmap]
rs11933302	1.00[CEU][hapmap]
rs1374936	0.81[ASN][1000 genomes]
rs1374937	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1584345	0.90[CHB][hapmap]
rs168161	0.97[ASN][1000 genomes]
rs17012279	1.00[CEU][hapmap]
rs17012291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1972969	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs2053772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2053774	0.88[ASN][1000 genomes]
rs2272777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2594276	0.83[CHB][hapmap]
rs2705617	0.81[ASN][1000 genomes]
rs340627	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340629	0.95[ASN][1000 genomes]
rs340631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340632	0.99[ASN][1000 genomes]
rs340635	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340640	0.95[ASN][1000 genomes]
rs340644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340645	0.95[ASN][1000 genomes]
rs340646	0.89[ASN][1000 genomes]
rs340649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4536897	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4693155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4693797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4693799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs58317309	0.91[ASN][1000 genomes]
rs6531943	0.95[ASN][1000 genomes]
rs6531944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6531945	1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs6531947	0.95[ASN][1000 genomes]
rs6815546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6822432	1.00[CEU][hapmap]
rs6824639	1.00[CEU][hapmap]
rs6848056	0.90[ASN][1000 genomes]
rs6853011	0.89[ASN][1000 genomes]
rs6855627	1.00[CEU][hapmap]
rs73837575	0.95[ASN][1000 genomes]
rs7685248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs895740	0.81[ASN][1000 genomes]
rs965824	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers 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 miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs340647	Hs.480174	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87929400-87946200	Weak transcription	Esophagus	oesophagus
2	chr4:87930600-87946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:87930600-87950000	Weak transcription	Fetal Stomach	stomach
4	chr4:87931000-87946600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:87931200-87943400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr4:87931800-87942600	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:87935600-87950200	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:87935800-87945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:87935800-87951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:87936000-87942600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:87936000-87950000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:87936400-87945000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:87937000-87946200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:87937000-87950400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:87937000-87951800	Weak transcription	NHEK	skin
16	chr4:87937000-87952000	Weak transcription	HMEC	breast
17	chr4:87937400-87946200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:87937600-87949800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:87938000-87942600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr4:87938000-87944800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:87938600-87942400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:87938600-87943000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr4:87938800-87942600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:87938800-87942800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr4:87939000-87942800	Enhancers	Brain Hippocampus Middle	brain
26	chr4:87939000-87943400	Enhancers	Primary B cells from peripheral blood	blood
27	chr4:87939200-87942600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr4:87939400-87942400	Weak transcription	HUVEC	blood vessel
29	chr4:87939400-87942600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:87939400-87944200	Weak transcription	Fetal Lung	lung
31	chr4:87939400-87950800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:87939600-87942800	Enhancers	Primary T cells from cord blood	blood
33	chr4:87939600-87944200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:87939600-87944600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:87939600-87944800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:87939600-87945200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:87939600-87946200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:87939600-87946400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:87939600-87946400	Weak transcription	Brain Angular Gyrus	brain
40	chr4:87939600-87950000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:87939600-87950400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:87939800-87944800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:87939800-87944800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:87939800-87945200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr4:87939800-87945200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:87939800-87945200	Weak transcription	NHDF-Ad	bronchial
47	chr4:87939800-87945800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:87939800-87945800	Weak transcription	Lung	lung
49	chr4:87939800-87946200	Weak transcription	Pancreas	Pancrea
50	chr4:87940200-87943400	Weak transcription	Stomach Smooth Muscle	stomach

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