Variant report

Variant	rs7617840
Chromosome Location	chr3:20162216-20162217
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20161544..20163874-chr3:20167611..20170613,4	K562	blood:
2	chr3:20161409..20163112-chr3:20165671..20167276,2	MCF-7	breast:
3	chr3:20160386..20162756-chr3:20172063..20173693,2	K562	blood:
4	chr3:20161536..20163874-chr3:20167611..20170613,5	K562	blood:
5	chr3:20154687..20157429-chr3:20160845..20162920,2	K562	blood:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12631457	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs12634506	0.87[ASN][1000 genomes]
rs12636078	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12636856	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs13072623	0.87[EUR][1000 genomes]
rs2929394	0.90[JPT][hapmap]
rs35801709	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4435661	0.82[ASN][1000 genomes]
rs4858767	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs55783650	0.93[EUR][1000 genomes]
rs58629324	0.85[ASN][1000 genomes]
rs6550351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs6763504	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6771737	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6772372	0.85[ASN][1000 genomes]
rs6804701	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7627847	0.80[JPT][hapmap]
rs9874923	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
14	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases
15	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
16	esv3394910	chr3:20150394-20203576	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	esv3334928	chr3:20150414-20203546	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
18	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
20	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7617840	RAB5A	cis	parietal	SCAN
rs7617840	KAT2B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
2	chr3:20128200-20175800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:20135200-20173800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:20139000-20164000	Weak transcription	Small Intestine	intestine
5	chr3:20141200-20167400	Weak transcription	HSMMtube	muscle
6	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:20142600-20189400	Weak transcription	Fetal Brain Male	brain
8	chr3:20146400-20163400	Weak transcription	Brain Germinal Matrix	brain
9	chr3:20147400-20169600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:20147600-20194200	Weak transcription	Dnd41	blood
11	chr3:20148000-20167000	Weak transcription	GM12878-XiMat	blood
12	chr3:20150800-20166200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:20151000-20196800	Weak transcription	Stomach Mucosa	stomach
14	chr3:20151200-20179000	Weak transcription	Fetal Kidney	kidney
15	chr3:20151600-20175800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:20152000-20182800	Weak transcription	Colonic Mucosa	Colon
17	chr3:20152200-20162600	Strong transcription	Thymus	Thymus
18	chr3:20152400-20162600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:20152600-20175200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:20152800-20170200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:20152800-20175000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr3:20152800-20176200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:20153400-20167200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:20153600-20169200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:20154000-20178400	Weak transcription	Psoas Muscle	Psoas
26	chr3:20154400-20164400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:20156400-20162600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:20156800-20163600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:20157000-20163800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:20157000-20165800	Weak transcription	Lung	lung
31	chr3:20157000-20165800	Weak transcription	Pancreas	Pancrea
32	chr3:20157000-20167200	Weak transcription	K562	blood
33	chr3:20157000-20178800	Weak transcription	HUVEC	blood vessel
34	chr3:20158000-20172400	Weak transcription	Fetal Brain Female	brain
35	chr3:20158800-20164000	Weak transcription	Ovary	ovary
36	chr3:20158800-20164200	Weak transcription	Placenta	Placenta
37	chr3:20158800-20169200	Weak transcription	Spleen	Spleen
38	chr3:20159200-20201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:20159400-20163400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:20159400-20163800	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:20159400-20164000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:20159400-20164200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:20159600-20164200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:20159600-20164200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:20160200-20166200	Strong transcription	Primary B cells from cord blood	blood
46	chr3:20160200-20170200	Strong transcription	Primary T cells from cord blood	blood
47	chr3:20160200-20170200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:20160400-20162400	Strong transcription	Fetal Lung	lung
49	chr3:20160400-20164800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:20160400-20166000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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