Variant report

Variant	rs263675
Chromosome Location	chr2:211037204-211037205
allele	A/G
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	E2F4	chr2:211036870-211037233	MCF10A-Er-Src	breast:	n/a	chr2:211036882-211036892
2	EGR1	chr2:211037032-211037244	K562	blood:	n/a	n/a
3	CHD1	chr2:211037089-211037394	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr2:211034433-211037263	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr2:211036864-211037221	K562	blood:	n/a	n/a
6	MXI1	chr2:211033551-211037427	SK-N-SH	brain:	n/a	chr2:211035505-211035514 chr2:211035573-211035582

No.	Distal block	Cell Line	Cell type
1	chr2:210866282..210870548-chr2:211034114..211037570,6	MCF-7	breast:
2	chr2:210866819..210870543-chr2:211034282..211037464,4	K562	blood:
3	chr2:208633171..208635747-chr2:211035528..211037623,2	MCF-7	breast:
4	chr2:210865937..210867928-chr2:211034610..211037287,3	MCF-7	breast:
5	chr2:210813951..210816642-chr2:211034382..211037269,2	K562	blood:
6	chr2:211032641..211035129-chr2:211036259..211038578,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263530	TF binding region
KANSL1L	TF binding region
ENSG00000163251	Chromatin interaction
ENSG00000197713	Chromatin interaction
ENSG00000144406	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10179268	1.00[ASN][1000 genomes]
rs10192315	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1155845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11675027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11678206	1.00[ASN][1000 genomes]
rs11682370	1.00[ASN][1000 genomes]
rs11686587	1.00[CHB][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs11688180	1.00[ASN][1000 genomes]
rs11688922	1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs12989455	1.00[ASN][1000 genomes]
rs12992714	1.00[ASN][1000 genomes]
rs13002602	1.00[ASN][1000 genomes]
rs13006132	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs13009071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs13009890	1.00[ASN][1000 genomes]
rs13011543	1.00[ASN][1000 genomes]
rs13015354	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13017647	1.00[ASN][1000 genomes]
rs13017752	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13018349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs13019613	1.00[ASN][1000 genomes]
rs13020232	1.00[ASN][1000 genomes]
rs13021055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13025700	1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs13415601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs1509568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs1509570	1.00[ASN][1000 genomes]
rs1509571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs1509572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16844058	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16844213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs2160020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2539005	1.00[ASN][1000 genomes]
rs263668	1.00[ASN][1000 genomes]
rs263680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs263681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs263686	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34334556	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34678259	1.00[ASN][1000 genomes]
rs35125543	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36080651	1.00[ASN][1000 genomes]
rs62202972	1.00[ASN][1000 genomes]
rs6435561	1.00[ASN][1000 genomes]
rs6714161	1.00[ASN][1000 genomes]
rs6716836	1.00[ASN][1000 genomes]
rs6732072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6732486	1.00[ASN][1000 genomes]
rs6732506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6735292	1.00[ASN][1000 genomes]
rs6749996	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs6754591	1.00[ASN][1000 genomes]
rs6760874	1.00[ASN][1000 genomes]
rs71350736	1.00[ASN][1000 genomes]
rs7557043	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7609345	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431969	chr2:210682494-211074494	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv1795338	chr2:210758078-211098113	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv1802749	chr2:210905194-211255611	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs263675	PLEKHM3	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211033000-211038000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:211033200-211037400	Active TSS	Right Atrium	heart
3	chr2:211033200-211037800	Active TSS	Fetal Kidney	kidney
4	chr2:211033200-211037800	Active TSS	Thymus	Thymus
5	chr2:211033400-211037800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:211033600-211037400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:211033800-211037400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:211033800-211037400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:211033800-211037400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:211033800-211037400	Active TSS	Psoas Muscle	Psoas
11	chr2:211033800-211037400	Active TSS	HSMMtube	muscle
12	chr2:211033800-211037600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:211034000-211037400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:211034000-211037400	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr2:211034000-211037400	Active TSS	NHDF-Ad	bronchial
16	chr2:211034000-211037600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:211034000-211037800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr2:211034200-211037400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr2:211034200-211037400	Active TSS	Right Ventricle	heart
20	chr2:211034400-211037400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr2:211034400-211037400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:211034400-211037800	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr2:211034400-211037800	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr2:211034800-211037400	Active TSS	Brain Angular Gyrus	brain
25	chr2:211036200-211037400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr2:211036200-211037400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:211036200-211037400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:211036400-211037400	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr2:211036400-211037800	Flanking Active TSS	Dnd41	blood
30	chr2:211036600-211037400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr2:211036800-211037400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:211036800-211037400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr2:211036800-211037400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr2:211036800-211037400	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr2:211036800-211037400	Flanking Active TSS	NH-A	brain
36	chr2:211036800-211037600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:211036800-211037600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:211036800-211037600	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr2:211037000-211037400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:211037000-211037400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr2:211037000-211037400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:211037000-211037400	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr2:211037000-211037800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr2:211037000-211037800	Flanking Active TSS	Liver	Liver
45	chr2:211037000-211042400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:211037000-211045000	Weak transcription	Gastric	stomach
47	chr2:211037000-211045000	Weak transcription	Pancreas	Pancrea
48	chr2:211037000-211046600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:211037200-211037400	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr2:211037200-211037400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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