Variant report

Variant	rs3817407
Chromosome Location	chr1:160788131-160788132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160786153..160788877-chr1:160788974..160791369,2	K562	blood:
2	chr1:160783146..160784738-chr1:160787422..160789189,2	K562	blood:
3	chr1:160787480..160789463-chr1:161085547..161088382,2	K562	blood:

Variant related genes	Relation type
ENSG00000122224	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158793	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11265492	0.90[EUR][1000 genomes]
rs12117689	0.96[EUR][1000 genomes]
rs12128261	0.89[EUR][1000 genomes]
rs12143580	0.93[EUR][1000 genomes]
rs1556517	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs1961611	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271967	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35132864	0.89[EUR][1000 genomes]
rs3766377	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4656270	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656271	0.96[EUR][1000 genomes]
rs4656932	0.95[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs4656933	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474918	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3817407	PPOX	cis	cerebellum	SCAN
rs3817407	ISG20L2	cis	parietal	SCAN
rs3817407	LMNA	cis	cerebellum	SCAN
rs3817407	ISG20L2	cis	cerebellum	SCAN
rs3817407	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs3817407	OR6K3	cis	cerebellum	SCAN
rs3817407	MRPL24	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160771000-160806600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:160777400-160789000	Strong transcription	Primary B cells from cord blood	blood
3	chr1:160778000-160795600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:160779800-160789200	Strong transcription	Primary T cells from cord blood	blood
7	chr1:160780000-160789800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:160781000-160789000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:160782400-160798200	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:160782600-160803200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:160782800-160789200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:160782800-160789600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:160783200-160788200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:160783400-160789400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:160783400-160791000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:160783600-160790000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:160783800-160798200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:160783800-160801000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:160783800-160803200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:160786600-160789400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:160786600-160792800	Weak transcription	Spleen	Spleen
22	chr1:160787600-160788600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:160787800-160788200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:160787800-160788200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:160787800-160788200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:160787800-160788400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:160787800-160788400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:160787800-160788600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:160787800-160788600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr1:160788000-160788400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:160788000-160788600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:160788000-160788600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:160788000-160788600	Enhancers	A549	lung
34	chr1:160788000-160788800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:160788000-160788800	Genic enhancers	Thymus	Thymus
36	chr1:160788000-160789000	Genic enhancers	Fetal Thymus	thymus

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