Variant report

Variant	rs1417580
Chromosome Location	chr1:161729749-161729750
allele	A/C
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	chr1:161725261..161728116-chr1:161728492..161730650,2	MCF-7	breast:
5	chr1:161718595..161726705-chr1:161728119..161739561,22	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]
rs1027701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1027702	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1063178	0.82[GIH][hapmap]
rs12026445	0.88[CHB][hapmap]
rs12116756	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12121310	0.82[GIH][hapmap]
rs12121500	0.82[GIH][hapmap]
rs12121522	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12564653	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745240	0.93[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1340981	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1417581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs2174208	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4657096	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4657097	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4657098	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6427624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6427625	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6427626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs1417580	PEAR1	cis	parietal	SCAN
rs1417580	DUSP12	cis	lymphoblastoid	seeQTL
rs1417580	ARHGEF11	cis	cerebellum	SCAN
rs1417580	C1orf61	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161720400-161734600	Weak transcription	Aorta	Aorta
2	chr1:161720600-161734600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:161720600-161734800	Weak transcription	Psoas Muscle	Psoas
4	chr1:161720600-161736000	Weak transcription	Spleen	Spleen
5	chr1:161720800-161734600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:161720800-161735000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:161720800-161735000	Weak transcription	Stomach Mucosa	stomach
8	chr1:161721000-161734600	Weak transcription	Right Ventricle	heart
9	chr1:161721000-161734600	Weak transcription	HSMMtube	muscle
10	chr1:161721000-161735000	Weak transcription	Fetal Heart	heart
11	chr1:161721200-161730000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:161721200-161730000	Strong transcription	Liver	Liver
13	chr1:161721200-161731000	Weak transcription	Right Atrium	heart
14	chr1:161721200-161732200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:161721200-161733800	Weak transcription	Pancreas	Pancrea
16	chr1:161721200-161734600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:161721200-161734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:161721400-161729800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:161721800-161730000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:161721800-161730200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:161722000-161730400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:161723200-161734800	Weak transcription	Colonic Mucosa	Colon
23	chr1:161723400-161730600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:161723400-161736000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:161724200-161735000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:161724600-161734600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:161724600-161734800	Weak transcription	Thymus	Thymus
28	chr1:161724600-161735000	Weak transcription	Fetal Brain Male	brain
29	chr1:161724600-161736000	Weak transcription	Small Intestine	intestine
30	chr1:161724800-161734600	Weak transcription	NHLF	lung
31	chr1:161724800-161736000	Weak transcription	Gastric	stomach
32	chr1:161725400-161733400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:161725400-161735000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:161725600-161729800	Strong transcription	Brain Germinal Matrix	brain
35	chr1:161725600-161730000	Strong transcription	Fetal Brain Female	brain
36	chr1:161725600-161733400	Weak transcription	HepG2	liver
37	chr1:161726000-161733600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:161726000-161734600	Weak transcription	Fetal Kidney	kidney
39	chr1:161726000-161735800	Weak transcription	Esophagus	oesophagus
40	chr1:161726600-161734600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:161726800-161733200	Weak transcription	K562	blood
42	chr1:161726800-161734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:161726800-161734600	Weak transcription	NHEK	skin
44	chr1:161726800-161734800	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:161726800-161734800	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:161726800-161734800	Weak transcription	Fetal Lung	lung
47	chr1:161726800-161735000	Weak transcription	Primary T cells from cord blood	blood
48	chr1:161726800-161735000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:161726800-161735800	Weak transcription	Lung	lung
50	chr1:161727000-161734600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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