Variant report

Variant	rs340649
Chromosome Location	chr4:87939237-87939238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87938501..87940925-chr4:87946524..87948135,2	K562	blood:
2	chr4:87938807..87941655-chr4:87943072..87944997,3	K562	blood:
3	chr4:87854648..87860283-chr4:87935219..87941983,10	K562	blood:
4	chr4:87926199..87928138-chr4:87938575..87940535,2	MCF-7	breast:
5	chr4:87938324..87940317-chr4:87979217..87981960,2	K562	blood:
6	chr4:87938104..87941655-chr4:87942635..87944997,3	K562	blood:
7	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:

Variant related genes	Relation type
ENSG00000235043	Chromatin interaction
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10003332	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10008600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs10022960	0.92[ASN][1000 genomes]
rs1374936	0.83[ASN][1000 genomes]
rs1374937	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1584345	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs168161	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012291	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972969	1.00[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2053774	0.91[ASN][1000 genomes]
rs2272777	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2594276	0.83[CHB][hapmap]
rs2705617	0.83[ASN][1000 genomes]
rs340627	0.97[ASN][1000 genomes]
rs340628	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340629	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340632	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs340635	1.00[ASN][1000 genomes]
rs340640	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340644	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340645	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340646	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs4536897	0.90[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs4693155	1.00[ASW][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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs4693799	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58317309	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6531943	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531944	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531945	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531947	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs6848056	0.92[ASN][1000 genomes]
rs6853011	0.92[ASN][1000 genomes]
rs72876089	0.89[EUR][1000 genomes]
rs73837575	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7685248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs895740	0.83[ASN][1000 genomes]
rs965824	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[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
rs340649	Hs.480174	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87929200-87939400	Weak transcription	Gastric	stomach
2	chr4:87929400-87946200	Weak transcription	Esophagus	oesophagus
3	chr4:87930600-87940600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:87930600-87946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:87930600-87950000	Weak transcription	Fetal Stomach	stomach
6	chr4:87930800-87940600	Weak transcription	Spleen	Spleen
7	chr4:87931000-87940800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr4:87931000-87940800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr4:87931000-87946600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:87931200-87940400	Enhancers	Primary B cells from cord blood	blood
11	chr4:87931200-87943400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr4:87931800-87942600	Enhancers	Primary hematopoietic stem cells	blood
13	chr4:87933200-87941000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:87934400-87940800	Enhancers	Fetal Intestine Small	intestine
15	chr4:87935200-87939400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:87935200-87940400	Enhancers	Liver	Liver
17	chr4:87935400-87942000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:87935600-87941000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr4:87935600-87950200	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:87935800-87941600	Enhancers	Dnd41	blood
21	chr4:87935800-87945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:87935800-87951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:87936000-87942600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:87936000-87950000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:87936400-87941600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr4:87936400-87945000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:87936800-87939800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:87937000-87939400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:87937000-87946200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr4:87937000-87950400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:87937000-87951800	Weak transcription	NHEK	skin
32	chr4:87937000-87952000	Weak transcription	HMEC	breast
33	chr4:87937200-87939600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:87937400-87939400	Weak transcription	Lung	lung
35	chr4:87937400-87939400	Weak transcription	Hela-S3	cervix
36	chr4:87937400-87940400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:87937400-87946200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:87937600-87941400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr4:87937600-87949800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr4:87937800-87939400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:87937800-87939600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr4:87937800-87939600	Enhancers	Osteobl	bone
43	chr4:87937800-87940800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr4:87938000-87941000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr4:87938000-87941200	Enhancers	Fetal Heart	heart
46	chr4:87938000-87942600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr4:87938000-87944800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr4:87938200-87939400	Weak transcription	Fetal Kidney	kidney
49	chr4:87938200-87939400	Enhancers	HUVEC	blood vessel
50	chr4:87938200-87939800	Enhancers	NHDF-Ad	bronchial

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