Variant report

Variant	rs2667961
Chromosome Location	chr1:220447602-220447603
allele	A/C
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	MAX	chr1:220447593-220448106	NB4	blood:	n/a	chr1:220447911-220447920
2	POLR2A	chr1:220447529-220447742	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr1:220447476-220448177	K562	blood:	n/a	chr1:220447911-220447920
4	CEBPB	chr1:220447567-220448085	H1-hESC	embryonic stem cell:	n/a	chr1:220447908-220447919 chr1:220447957-220447970

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: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1033107	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10495144	0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10863535	0.85[AMR][1000 genomes]
rs11118502	0.85[AMR][1000 genomes]
rs11118505	0.85[AMR][1000 genomes]
rs12062286	0.85[AFR][1000 genomes]
rs12066759	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070983	0.85[AMR][1000 genomes]
rs2491268	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2667960	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2667962	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2667963	1.00[AMR][1000 genomes]
rs2789791	0.85[AMR][1000 genomes]
rs2808010	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2808017	0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2814493	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4445474	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9431233	0.87[AFR][1000 genomes]

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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220446200-220448200	Weak transcription	Pancreas	Pancrea
2	chr1:220446400-220448400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr1:220446600-220447800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:220446600-220447800	Weak transcription	Brain Germinal Matrix	brain
5	chr1:220446600-220447800	Weak transcription	HMEC	breast
6	chr1:220446600-220447800	Weak transcription	K562	blood
7	chr1:220446600-220448200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:220446600-220448400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:220446600-220448600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:220446600-220448600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:220446600-220448600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:220446600-220448600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:220446600-220448600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr1:220446600-220448800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:220446600-220449000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:220446600-220449800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:220446600-220451800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:220446800-220448000	Weak transcription	Dnd41	blood
19	chr1:220446800-220448200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:220446800-220449000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:220447000-220448200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:220447200-220448200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:220447200-220448400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr1:220447200-220448400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:220447200-220448600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr1:220447400-220452400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:220447600-220447800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr1:220447600-220447800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr1:220447600-220448000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr1:220447600-220448000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:220447600-220448000	Enhancers	Brain Anterior Caudate	brain
32	chr1:220447600-220448000	Enhancers	NH-A	brain
33	chr1:220447600-220448200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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