Variant report

Variant	rs164861
Chromosome Location	chr5:14262535-14262536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14260701..14263279-chr5:14263395..14266329,3	K562	blood:
2	chr5:14255845..14258384-chr5:14262309..14265414,3	MCF-7	breast:
3	chr5:14262017..14264062-chr5:14267525..14269616,2	K562	blood:
4	chr5:14152278..14154256-chr5:14262116..14264900,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11747048	1.00[CHB][hapmap]
rs13175673	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13184211	1.00[CHB][hapmap]
rs13184670	1.00[CHB][hapmap]
rs17299045	1.00[CHB][hapmap]
rs17302408	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs187125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434605	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs245577	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591277	0.99[EUR][1000 genomes]
rs26057	1.00[CHB][hapmap]
rs26058	1.00[CHB][hapmap]
rs26059	1.00[CHB][hapmap]
rs26061	1.00[CHB][hapmap]
rs2607077	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607078	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697663	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27665	1.00[CHB][hapmap]
rs28010	1.00[CHB][hapmap]
rs30616	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs30617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32339	1.00[CHB][hapmap]
rs32341	1.00[CHB][hapmap]
rs32390	1.00[CHB][hapmap]
rs32394	1.00[CHB][hapmap]
rs354285	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs354298	1.00[CHB][hapmap]
rs354300	1.00[CHB][hapmap]
rs354305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354308	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354312	1.00[CHB][hapmap]
rs3849082	1.00[CHB][hapmap]
rs39856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42485	1.00[ASN][1000 genomes]
rs4702028	1.00[CHB][hapmap]
rs706271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773703	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs773763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799025	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897724	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897726	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923616	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs164861	CHMP7	trans	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14253800-14264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:14256200-14264200	Enhancers	H1 Cell Line	embryonic stem cell
3	chr5:14256400-14265400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:14256600-14264400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:14257000-14264600	Enhancers	NH-A	brain
6	chr5:14257200-14264800	Weak transcription	Stomach Mucosa	stomach
7	chr5:14257200-14265000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:14258400-14264600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:14258800-14264400	Weak transcription	Fetal Intestine Small	intestine
10	chr5:14258800-14265000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr5:14259000-14264600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:14259000-14264600	Weak transcription	Fetal Brain Male	brain
13	chr5:14259000-14268400	Weak transcription	Esophagus	oesophagus
14	chr5:14259200-14263400	Weak transcription	HepG2	liver
15	chr5:14259200-14263800	Weak transcription	Primary B cells from cord blood	blood
16	chr5:14259200-14264400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:14259200-14264600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr5:14259200-14264600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:14259200-14264600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:14259200-14264600	Enhancers	Brain Germinal Matrix	brain
21	chr5:14259200-14264600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:14259200-14264600	Weak transcription	Psoas Muscle	Psoas
23	chr5:14259200-14264600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr5:14259200-14264600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:14259200-14265000	Weak transcription	Colonic Mucosa	Colon
26	chr5:14259200-14267400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:14259200-14268400	Weak transcription	Spleen	Spleen
28	chr5:14259200-14268600	Weak transcription	Gastric	stomach
29	chr5:14259400-14264400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:14259600-14263800	Enhancers	A549	lung
31	chr5:14259600-14264600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr5:14259600-14264800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:14259600-14265000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr5:14259800-14262800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:14259800-14263200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:14259800-14264800	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:14260000-14263800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:14260000-14264000	Genic enhancers	HSMM	muscle
39	chr5:14260000-14264600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr5:14260200-14262800	Enhancers	HSMMtube	muscle
41	chr5:14260400-14265000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr5:14260600-14264600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr5:14260800-14263000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:14260800-14264600	Enhancers	Fetal Thymus	thymus
45	chr5:14261000-14262800	Enhancers	Stomach Smooth Muscle	stomach
46	chr5:14261000-14263000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:14261000-14263000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:14261000-14263000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr5:14261000-14263000	Enhancers	Left Ventricle	heart
50	chr5:14261000-14263200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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