Variant report

Variant	rs12032631
Chromosome Location	chr1:155995080-155995081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155987340..155997180-chr1:156020881..156026682,16	K562	blood:
2	chr1:155989952..155992732-chr1:155994341..155996999,4	K562	blood:
3	chr1:155993386..155995708-chr1:156048411..156050502,2	MCF-7	breast:
4	chr1:155989710..155992732-chr1:155994151..155995947,4	K562	blood:
5	chr1:155994718..155996302-chr1:156009126..156010718,2	MCF-7	breast:
6	chr1:155994840..155997180-chr1:156020881..156023261,2	K562	blood:
7	chr1:155994276..155996728-chr1:156001634..156004616,2	MCF-7	breast:
8	chr1:155988173..156003032-chr1:156020965..156026206,23	MCF-7	breast:
9	chr1:155994337..155996997-chr1:156001255..156005019,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000116586	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000163479	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10908486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11577179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11582305	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12043212	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12128541	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1475766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17381047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17385065	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1966243	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2095402	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2297792	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2364400	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886070	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34126883	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34444588	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34995046	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4330912	0.82[AMR][1000 genomes]
rs4661079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6668204	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517202	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12032631	YY1AP1	cis	cerebellum	SCAN
rs12032631	SPRR3	cis	parietal	SCAN
rs12032631	RIT1	cis	cerebellum	SCAN
rs12032631	UBQLN4	trans	parietal	SCAN
rs12032631	ROBLD3	cis	parietal	SCAN
rs12032631	PRUNE	cis	cerebellum	SCAN
rs12032631	SNX27	cis	parietal	SCAN
rs12032631	SYT11	cis	parietal	SCAN
rs12032631	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155990800-155995800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:155990800-156006000	Weak transcription	Spleen	Spleen
3	chr1:155990800-156006800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:155991000-155995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:155991000-155995600	Weak transcription	Placenta	Placenta
6	chr1:155991000-155995800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:155991000-156002600	Weak transcription	NHLF	lung
8	chr1:155991000-156005800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:155991000-156011600	Weak transcription	Colonic Mucosa	Colon
10	chr1:155991200-155995600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:155991200-155995600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:155991200-155995800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:155991200-155995800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:155991200-155995800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:155991200-155995800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:155991200-155995800	Weak transcription	A549	lung
17	chr1:155991200-155995800	Weak transcription	HMEC	breast
18	chr1:155991200-155995800	Weak transcription	HUVEC	blood vessel
19	chr1:155991200-156002800	Weak transcription	NH-A	brain
20	chr1:155991200-156005600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:155991200-156005600	Weak transcription	Brain Angular Gyrus	brain
22	chr1:155991200-156005800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:155991200-156005800	Weak transcription	Liver	Liver
24	chr1:155991200-156005800	Weak transcription	Brain Anterior Caudate	brain
25	chr1:155991200-156005800	Weak transcription	Fetal Thymus	thymus
26	chr1:155991200-156006000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:155991200-156006000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:155991200-156006600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:155991200-156006600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:155991200-156010800	Weak transcription	Fetal Heart	heart
31	chr1:155991200-156020000	Weak transcription	GM12878-XiMat	blood
32	chr1:155992200-156005800	Weak transcription	Dnd41	blood
33	chr1:155993800-155995800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr1:155994200-155995600	Enhancers	Fetal Intestine Small	intestine
35	chr1:155994200-155996200	Enhancers	Fetal Intestine Large	intestine
36	chr1:155994600-155995200	Flanking Active TSS	HepG2	liver
37	chr1:155994800-155995600	Enhancers	K562	blood
38	chr1:155994800-156005800	Weak transcription	Brain Germinal Matrix	brain
39	chr1:155995000-155996000	Enhancers	Duodenum Mucosa	Duodenum

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