Variant report

Variant	rs2781233
Chromosome Location	chr1:10529194-10529195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10526639..10529989-chr1:10530348..10533408,3	K562	blood:
2	chr1:10528950..10534210-chr1:10534257..10537658,6	K562	blood:
3	chr1:10527442..10529294-chr1:10531066..10533842,2	K562	blood:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction
ENSG00000160049	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10746494	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10864458	0.80[AFR][1000 genomes]
rs11121579	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11584327	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs1203122	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565133	0.96[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1307485	0.96[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1307487	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17035189	0.84[CEU][hapmap]
rs1750349	0.81[ASN][1000 genomes]
rs1760664	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2186949	0.83[EUR][1000 genomes]
rs2274985	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs2483679	0.82[JPT][hapmap]
rs2483684	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36013615	0.81[EUR][1000 genomes]
rs475549	0.84[EUR][1000 genomes]
rs481571	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs491880	0.96[CEU][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs505141	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs519472	0.86[EUR][1000 genomes]
rs520964	0.83[EUR][1000 genomes]
rs522029	0.84[EUR][1000 genomes]
rs522280	0.86[EUR][1000 genomes]
rs524150	0.86[EUR][1000 genomes]
rs528713	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs583515	0.83[EUR][1000 genomes]
rs586223	0.92[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs597441	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs604369	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs628462	0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs632690	0.83[EUR][1000 genomes]
rs634358	0.96[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs643400	0.80[EUR][1000 genomes]
rs649101	0.92[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs649639	0.86[EUR][1000 genomes]
rs655271	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs663864	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs666583	0.84[EUR][1000 genomes]
rs670666	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs672606	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673254	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs678850	0.86[EUR][1000 genomes]
rs681448	0.83[EUR][1000 genomes]
rs684016	0.96[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs685746	0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs7419116	0.81[CEU][hapmap]
rs7548453	0.84[CEU][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2781233	PLEKHG5	cis	parietal	SCAN
rs2781233	APITD1	cis	cerebellum	SCAN
rs2781233	KIAA2013	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10499200-10531400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10510600-10531600	Weak transcription	Right Atrium	heart
3	chr1:10511600-10531600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:10512400-10531200	Weak transcription	Fetal Brain Male	brain
5	chr1:10516000-10530200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:10516000-10530200	Strong transcription	Fetal Stomach	stomach
7	chr1:10516800-10530200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:10516800-10530400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:10517000-10529800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr1:10517200-10529400	Strong transcription	Brain Germinal Matrix	brain
11	chr1:10517400-10531600	Weak transcription	Fetal Heart	heart
12	chr1:10517600-10529600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:10517800-10530400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:10518000-10529200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:10518000-10529600	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr1:10518000-10529600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:10518000-10530400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:10518200-10530200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:10519000-10529200	Strong transcription	Fetal Thymus	thymus
20	chr1:10519000-10529400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:10519000-10529800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:10519200-10529600	Strong transcription	Thymus	Thymus
23	chr1:10519600-10530600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:10519800-10531400	Weak transcription	Stomach Mucosa	stomach
25	chr1:10520000-10531200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:10520000-10531400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:10520200-10531200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:10520400-10529600	Strong transcription	Brain Hippocampus Middle	brain
29	chr1:10520400-10530000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:10520600-10529400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:10520600-10529600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:10520600-10530200	Strong transcription	Fetal Intestine Small	intestine
33	chr1:10520600-10530400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:10521000-10529400	Strong transcription	Ovary	ovary
35	chr1:10521000-10529600	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:10521000-10529600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:10521000-10529600	Strong transcription	Dnd41	blood
38	chr1:10521000-10529800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr1:10521000-10530200	Strong transcription	Placenta	Placenta
40	chr1:10521200-10529200	Strong transcription	Pancreas	Pancrea
41	chr1:10521200-10529400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:10521200-10529400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:10521200-10529400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:10521200-10529400	Strong transcription	Fetal Lung	lung
45	chr1:10521200-10529400	Strong transcription	Gastric	stomach
46	chr1:10521200-10529400	Strong transcription	Left Ventricle	heart
47	chr1:10521200-10529400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:10521200-10529400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:10521200-10529400	Strong transcription	NHLF	lung
50	chr1:10521200-10529600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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