Variant report

Variant	rs6929403
Chromosome Location	chr6:119346912-119346913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119254679..119257709-chr6:119345314..119348815,3	K562	blood:
2	chr6:119346161..119349573-chr6:119350909..119353024,3	K562	blood:
3	chr6:119345576..119347207-chr6:119354495..119357299,2	K562	blood:
4	chr6:119344453..119347404-chr6:119349767..119351941,2	K562	blood:

Variant related genes	Relation type
ENSG00000111877	Chromatin interaction
ENSG00000253194	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1022707	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs1022708	0.90[CHB][hapmap]
rs10499090	0.83[ASN][1000 genomes]
rs11153782	0.90[CHB][hapmap]
rs12527363	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12664251	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885125	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2145569	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2357030	0.84[JPT][hapmap]
rs284919	0.84[JPT][hapmap]
rs2884078	0.95[JPT][hapmap]
rs3756940	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4946372	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs4946373	0.90[CHB][hapmap]
rs4946382	0.90[CHB][hapmap]
rs4946386	0.83[ASN][1000 genomes]
rs4946387	0.99[ASN][1000 genomes]
rs6904381	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs6918844	0.89[CHB][hapmap]
rs6931074	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6939937	0.90[CHB][hapmap]
rs72970476	0.83[ASN][1000 genomes]
rs7381535	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs9320671	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs9374777	0.95[JPT][hapmap]
rs9387621	0.90[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]
rs9387624	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9387626	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9387628	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9401106	0.90[CHB][hapmap]
rs9401118	0.95[JPT][hapmap]
rs988098	0.90[CHB][hapmap];0.81[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030400	chr6:119320153-119433830	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6929403	MCM9	cis	lymphoblastoid	seeQTL
rs6929403	MCMDC1	cis	multi-tissue	Pritchard
rs6929403	MCM9	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119314400-119364400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:119325400-119349600	Weak transcription	Brain Angular Gyrus	brain
3	chr6:119328600-119348800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:119330400-119347000	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:119331400-119349800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:119331400-119356000	Weak transcription	Ovary	ovary
7	chr6:119331600-119349200	Weak transcription	Adipose Nuclei	Adipose
8	chr6:119331600-119355800	Weak transcription	K562	blood
9	chr6:119334200-119355800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:119334800-119347000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:119339400-119356200	Weak transcription	Placenta	Placenta
12	chr6:119340200-119347000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:119341400-119356200	Weak transcription	Fetal Stomach	stomach
14	chr6:119343400-119356400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:119343600-119355800	Weak transcription	Fetal Intestine Small	intestine
16	chr6:119343800-119349800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr6:119344000-119347000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:119344600-119348400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:119345200-119349200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:119345200-119350400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:119345600-119347000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:119345800-119349600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr6:119345800-119350200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr6:119346000-119347000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:119346000-119348200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr6:119346000-119350000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:119346200-119349000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:119346400-119347600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:119346600-119349800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr6:119346600-119350000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:119346800-119347400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:119346800-119347400	Enhancers	Brain Cingulate Gyrus	brain
33	chr6:119346800-119347400	Enhancers	HSMMtube	muscle
34	chr6:119346800-119347800	Enhancers	HUES64 Cell Line	embryonic stem cell

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