Variant report

Variant	rs12745240
Chromosome Location	chr1:161728001-161728002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161717547..161721793-chr1:161722241..161732156,16	K562	blood:
2	chr1:161726675..161730185-chr1:162535816..162538493,3	K562	blood:
3	chr1:161727932..161729878-chr1:161731559..161734430,3	K562	blood:
4	chr1:161708003..161709777-chr1:161726766..161729358,2	K562	blood:
5	chr1:161725261..161728116-chr1:161728492..161730650,2	MCF-7	breast:
6	chr1:161718657..161721978-chr1:161725232..161728078,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117143	Chromatin interaction
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1027702	0.81[GIH][hapmap]
rs1063178	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10917821	0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12121310	0.94[ASW][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs12121500	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12121522	0.81[GIH][hapmap]
rs12564653	0.80[EUR][1000 genomes]
rs1340981	0.81[GIH][hapmap]
rs1417580	0.93[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1417581	0.82[EUR][1000 genomes]
rs16852851	0.89[YRI][hapmap]
rs2066247	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs2174209	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34963459	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35541527	0.89[YRI][hapmap]
rs4532807	0.85[YRI][hapmap]
rs4656332	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4657096	0.81[GIH][hapmap]
rs6427626	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs71634909	0.84[AFR][1000 genomes]
rs953301	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12745240	PEAR1	cis	parietal	SCAN
rs12745240	ARHGEF11	cis	cerebellum	SCAN
rs12745240	FCRL6	cis	cerebellum	SCAN
rs12745240	C1orf61	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161720400-161734600	Weak transcription	Aorta	Aorta
2	chr1:161720600-161728800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:161720600-161734600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:161720600-161734800	Weak transcription	Psoas Muscle	Psoas
5	chr1:161720600-161736000	Weak transcription	Spleen	Spleen
6	chr1:161720800-161734600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:161720800-161735000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:161720800-161735000	Weak transcription	Stomach Mucosa	stomach
9	chr1:161721000-161728200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:161721000-161728800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:161721000-161728800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:161721000-161728800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:161721000-161728800	Strong transcription	Placenta	Placenta
14	chr1:161721000-161734600	Weak transcription	Right Ventricle	heart
15	chr1:161721000-161734600	Weak transcription	HSMMtube	muscle
16	chr1:161721000-161735000	Weak transcription	Fetal Heart	heart
17	chr1:161721200-161728600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:161721200-161728600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:161721200-161728600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:161721200-161728600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:161721200-161728800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:161721200-161728800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:161721200-161728800	Strong transcription	Fetal Intestine Large	intestine
24	chr1:161721200-161729000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:161721200-161729000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:161721200-161729600	Strong transcription	Fetal Muscle Leg	muscle
27	chr1:161721200-161730000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:161721200-161730000	Strong transcription	Liver	Liver
29	chr1:161721200-161731000	Weak transcription	Right Atrium	heart
30	chr1:161721200-161732200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:161721200-161733800	Weak transcription	Pancreas	Pancrea
32	chr1:161721200-161734600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:161721200-161734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:161721400-161728600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:161721400-161728600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:161721400-161728600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:161721400-161728600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:161721400-161728600	Strong transcription	HSMM	muscle
39	chr1:161721400-161728600	Strong transcription	HUVEC	blood vessel
40	chr1:161721400-161728600	Strong transcription	NH-A	brain
41	chr1:161721400-161728800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:161721400-161728800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:161721400-161728800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:161721400-161728800	Strong transcription	Osteobl	bone
45	chr1:161721400-161729800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:161721600-161728600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:161721600-161728800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:161721600-161728800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:161721600-161728800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:161721600-161728800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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