Variant report

Variant	rs4671535
Chromosome Location	chr2:64071232-64071233
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	POLR2A	chr2:64066467-64077414	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD1	chr2:64067067-64074747	H1-hESC	embryonic stem cell:	n/a	chr2:64068850-64068860 chr2:64068822-64068832 chr2:64068878-64068888 chr2:64067996-64068006
3	SIN3A	chr2:64067165-64073428	H1-hESC	embryonic stem cell:	n/a	chr2:64073388-64073396
4	POLR2A	chr2:64070910-64071483	H1-hESC	embryonic stem cell:	n/a	n/a
5	ATF2	chr2:64070865-64071334	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:64070585-64071258	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:64067047-64071252	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr2:64070928-64071474	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF7	chr2:64067139-64075620	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64066407..64070482-chr2:64071096..64075382,10	MCF-7	breast:
2	chr2:64070153..64071712-chr2:64106669..64108533,2	K562	blood:

Variant related genes	Relation type
UGP2	TF binding region
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10166971	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10175674	0.89[CHB][hapmap]
rs12474366	1.00[ASN][1000 genomes]
rs12475294	1.00[ASN][1000 genomes]
rs12988017	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs12993544	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12999675	0.93[ASN][1000 genomes]
rs13009774	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs13010817	1.00[ASN][1000 genomes]
rs13028805	1.00[ASN][1000 genomes]
rs13034260	1.00[ASN][1000 genomes]
rs1345479	0.91[ASN][1000 genomes]
rs17555655	0.88[ASN][1000 genomes]
rs17620012	0.93[ASN][1000 genomes]
rs2034802	1.00[ASW][hapmap]
rs2287361	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34145077	0.91[ASN][1000 genomes]
rs34196086	0.93[ASN][1000 genomes]
rs34200806	0.88[ASN][1000 genomes]
rs34239752	0.98[ASN][1000 genomes]
rs34512058	1.00[ASN][1000 genomes]
rs34900788	1.00[ASN][1000 genomes]
rs35058898	1.00[ASN][1000 genomes]
rs35253921	1.00[ASN][1000 genomes]
rs35521527	0.88[ASN][1000 genomes]
rs35552326	1.00[ASN][1000 genomes]
rs36099158	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs3934536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4482470	0.91[ASN][1000 genomes]
rs4544421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4599090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4671072	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs4671534	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671537	0.88[ASN][1000 genomes]
rs66595136	0.88[ASN][1000 genomes]
rs66660401	0.84[ASN][1000 genomes]
rs67366434	1.00[ASN][1000 genomes]
rs67962955	0.88[ASN][1000 genomes]
rs72808231	1.00[ASN][1000 genomes]
rs893779	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][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	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4671535	PEX13	cis	cerebellum	SCAN
rs4671535	CCT4	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64067000-64073200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr2:64067000-64075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:64067000-64076400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:64067200-64071600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:64067200-64071800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:64067200-64072000	Active TSS	Aorta	Aorta
7	chr2:64067200-64072000	Active TSS	Fetal Muscle Trunk	muscle
8	chr2:64067200-64072200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:64067200-64072200	Active TSS	Colonic Mucosa	Colon
10	chr2:64067200-64072400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:64067200-64073200	Active TSS	Left Ventricle	heart
12	chr2:64067200-64073400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:64067400-64071400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:64067400-64072200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:64067400-64074000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr2:64067600-64071400	Active TSS	HSMMtube	muscle
17	chr2:64067600-64071600	Active TSS	Psoas Muscle	Psoas
18	chr2:64067600-64071600	Active TSS	NHLF	lung
19	chr2:64067600-64072800	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr2:64067600-64074000	Active TSS	Right Ventricle	heart
21	chr2:64067800-64071600	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr2:64067800-64071800	Active TSS	Fetal Muscle Leg	muscle
23	chr2:64068000-64071600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:64069000-64071600	Active TSS	Right Atrium	heart
25	chr2:64069000-64071800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:64069000-64072800	Weak transcription	Spleen	Spleen
27	chr2:64069200-64071400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr2:64069400-64072000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr2:64069400-64072000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:64069400-64072600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:64069400-64073400	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr2:64069400-64074600	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr2:64069600-64071400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:64069800-64073200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
35	chr2:64070000-64072200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:64070000-64073600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:64070000-64082800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:64070200-64072200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr2:64070200-64072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr2:64070200-64076400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:64070200-64084600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:64070200-64103000	Weak transcription	Gastric	stomach
43	chr2:64070400-64071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:64070400-64071800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr2:64070400-64071800	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr2:64070400-64072400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr2:64070400-64075800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:64070600-64071400	Enhancers	Colon Smooth Muscle	Colon
49	chr2:64070600-64071600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:64070600-64071600	Enhancers	Stomach Mucosa	stomach

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