Variant report

Variant	rs6690426
Chromosome Location	chr1:220446809-220446810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr1:220443617-220447007	K562	blood:	n/a	chr1:220444866-220444875 chr1:220445240-220445252

No.	Distal block	Cell Line	Cell type
1	chr1:220446026..220449283-chr1:220451004..220455196,4	K562	blood:
2	chr1:220396718..220399259-chr1:220445966..220447617,2	MCF-7	breast:
3	chr1:220445957..220448646-chr1:220450817..220453082,3	K562	blood:
4	chr1:220445870..220448039-chr1:220448307..220450938,3	K562	blood:

Variant related genes	Relation type
RAB3GAP2	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10127631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779401	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10863539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10863540	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11118506	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118510	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118513	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11586671	1.00[EUR][1000 genomes]
rs12022336	0.82[ASN][1000 genomes]
rs12025326	0.82[ASN][1000 genomes]
rs12025702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12026270	0.82[ASN][1000 genomes]
rs12030504	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032536	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12032738	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12033612	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12037712	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12039349	0.82[ASN][1000 genomes]
rs12040095	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12043920	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12086105	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12086760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28650887	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56357312	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6703091	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73087829	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73095623	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73095636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098569	0.82[ASN][1000 genomes]
rs73098579	0.82[ASN][1000 genomes]
rs874331	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220446200-220447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:220446200-220447400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:220446200-220447600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:220446200-220448200	Weak transcription	Pancreas	Pancrea
5	chr1:220446400-220447200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:220446400-220447600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:220446400-220448400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr1:220446600-220447000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:220446600-220447200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:220446600-220447400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:220446600-220447600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:220446600-220447600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:220446600-220447600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:220446600-220447600	Weak transcription	Adipose Nuclei	Adipose
15	chr1:220446600-220447600	Weak transcription	Brain Anterior Caudate	brain
16	chr1:220446600-220447600	Weak transcription	NH-A	brain
17	chr1:220446600-220447800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:220446600-220447800	Weak transcription	Brain Germinal Matrix	brain
19	chr1:220446600-220447800	Weak transcription	HMEC	breast
20	chr1:220446600-220447800	Weak transcription	K562	blood
21	chr1:220446600-220448200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:220446600-220448400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:220446600-220448600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:220446600-220448600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:220446600-220448600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:220446600-220448600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:220446600-220448600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:220446600-220448800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:220446600-220449000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:220446600-220449800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:220446600-220451800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:220446800-220447200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:220446800-220448000	Weak transcription	Dnd41	blood
34	chr1:220446800-220448200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr1:220446800-220449000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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