Variant report

Variant	rs4132646
Chromosome Location	chr1:151534142-151534143
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	1:151516085-151535167..1:151592347-151603110	GM12878	blood:
2	chr1:151528431..151530399-chr1:151533235..151535890,2	K562	blood:
3	1:151402394-151411623..1:151516085-151535167	GM12878	blood:
4	chr1:151510867..151515069-chr1:151533037..151539348,7	MCF-7	breast:
5	chr1:151532006..151534507-chr1:151547332..151548889,2	MCF-7	breast:
6	1:151171193-151178589..1:151516085-151535167	GM12878	blood:
7	chr1:151510534..151515854-chr1:151533093..151539013,11	MCF-7	breast:
8	chr1:151528431..151531724-chr1:151533235..151535890,3	K562	blood:

Variant related genes	Relation type
ENSG00000206635	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11204848	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12217027	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12746522	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12746531	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1573129	0.86[LWK][hapmap]
rs2185838	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3790507	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970961	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4970962	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587597	0.92[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6673116	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6691736	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552458	0.86[LWK][hapmap]
rs9645404	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4132646	CTSS	cis	cerebellum	SCAN
rs4132646	NPR1	cis	cerebellum	SCAN
rs4132646	LINGO4	cis	cerebellum	SCAN
rs4132646	LCE1C	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151514400-151540800	Weak transcription	Brain Angular Gyrus	brain
2	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
3	chr1:151515600-151534400	Weak transcription	Brain Germinal Matrix	brain
4	chr1:151520200-151534200	Weak transcription	Fetal Stomach	stomach
5	chr1:151520200-151536600	Weak transcription	Ovary	ovary
6	chr1:151520400-151534200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:151520400-151535800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:151520400-151536600	Weak transcription	Adipose Nuclei	Adipose
9	chr1:151520400-151536800	Weak transcription	Aorta	Aorta
10	chr1:151520600-151536000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:151520600-151536800	Weak transcription	Lung	lung
12	chr1:151520600-151542000	Weak transcription	Right Ventricle	heart
13	chr1:151520600-151545200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:151520800-151535600	Weak transcription	Colonic Mucosa	Colon
15	chr1:151520800-151535600	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:151521600-151537800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:151521600-151538600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:151521800-151541800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:151521800-151559000	Weak transcription	Small Intestine	intestine
20	chr1:151522000-151534200	Weak transcription	Pancreas	Pancrea
21	chr1:151522000-151534800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:151522000-151535000	Weak transcription	HSMMtube	muscle
23	chr1:151522000-151536600	Weak transcription	Esophagus	oesophagus
24	chr1:151522000-151537600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:151522200-151536200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:151522200-151537800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:151522200-151537800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:151522400-151534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:151522400-151540800	Weak transcription	Stomach Mucosa	stomach
30	chr1:151522600-151534400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:151522600-151534600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:151522600-151536000	Weak transcription	Hela-S3	cervix
33	chr1:151522600-151536400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:151522800-151534200	Weak transcription	Fetal Intestine Large	intestine
35	chr1:151522800-151534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:151522800-151536400	Weak transcription	HepG2	liver
37	chr1:151524200-151537600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:151525000-151536600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:151526400-151534200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:151526400-151536400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:151526400-151536600	Weak transcription	NHLF	lung
42	chr1:151526600-151536800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:151526800-151536600	Weak transcription	NH-A	brain
44	chr1:151526800-151536600	Weak transcription	Osteobl	bone
45	chr1:151526800-151538600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:151528200-151536800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:151529400-151536000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:151529400-151536600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:151529600-151535800	Strong transcription	NHEK	skin
50	chr1:151530200-151540800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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