Variant report

Variant	rs1816618
Chromosome Location	chr2:64447884-64447885
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64401304..64403227-chr2:64446509..64448763,2	MCF-7	breast:
2	chr2:64437286..64442036-chr2:64442990..64448045,5	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1019685	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1019686	0.96[CEU][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1025209	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1025210	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10496110	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125993	0.83[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11125994	0.89[ASN][1000 genomes]
rs13399701	0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1365482	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1370388	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1529101	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1582792	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1816617	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963382	0.81[EUR][1000 genomes]
rs2059634	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2247947	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2251764	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2555425	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2555426	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2555434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2555436	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2555437	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2555438	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2555441	0.81[EUR][1000 genomes]
rs2555442	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2698523	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2698541	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2951018	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3731961	0.80[JPT][hapmap]
rs6750096	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs871776	1.00[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	nsv1004899	chr2:64369300-64513607	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	nsv535769	chr2:64369300-64513607	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv1015084	chr2:64369734-64512286	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	nsv874237	chr2:64402689-64479060	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1816618	PEX13	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64438200-64448200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:64440400-64455000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:64441200-64448800	Weak transcription	Pancreas	Pancrea
4	chr2:64441400-64450400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:64441400-64455200	Weak transcription	Esophagus	oesophagus
6	chr2:64442000-64449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:64442200-64449000	Weak transcription	Fetal Intestine Large	intestine
8	chr2:64442400-64454200	Weak transcription	Fetal Kidney	kidney
9	chr2:64442400-64454600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:64442800-64450200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:64443200-64450400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:64443800-64449600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:64445400-64448200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:64445600-64448000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr2:64445600-64449000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:64446200-64451800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr2:64446400-64448000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:64446400-64448000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr2:64446400-64448200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:64446400-64449400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr2:64446400-64449600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr2:64446400-64450400	Enhancers	Brain Substantia Nigra	brain
23	chr2:64446400-64451000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:64446400-64451400	Enhancers	Primary T cells from cord blood	blood
25	chr2:64446400-64451800	Enhancers	Primary B cells from peripheral blood	blood
26	chr2:64446600-64448000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:64446800-64448200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr2:64446800-64448200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr2:64446800-64448200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr2:64446800-64448400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:64446800-64449000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr2:64446800-64449200	Enhancers	Brain Hippocampus Middle	brain
33	chr2:64446800-64449400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr2:64446800-64450600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:64446800-64450800	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:64447000-64448000	Enhancers	H9 Cell Line	embryonic stem cell
37	chr2:64447000-64448000	Enhancers	Primary hematopoietic stem cells	blood
38	chr2:64447000-64448000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:64447000-64448200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr2:64447000-64448200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr2:64447000-64448400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:64447000-64450200	Enhancers	Brain Angular Gyrus	brain
43	chr2:64447200-64448000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:64447200-64448200	Enhancers	K562	blood
45	chr2:64447200-64448400	Enhancers	Psoas Muscle	Psoas
46	chr2:64447200-64450000	Enhancers	Stomach Mucosa	stomach
47	chr2:64447200-64450200	Enhancers	GM12878-XiMat	blood
48	chr2:64447200-64450600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr2:64447200-64450800	Enhancers	Colon Smooth Muscle	Colon
50	chr2:64447400-64448600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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