Variant report

Variant	rs6427627
Chromosome Location	chr1:154359179-154359180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154297622..154300482-chr1:154357910..154359752,2	K562	blood:
2	chr1:154356874..154359380-chr1:154375145..154377788,2	K562	blood:
3	chr1:154323094..154325358-chr1:154357953..154361791,3	K562	blood:

Variant related genes	Relation type
ENSG00000143515	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10908835	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265606	0.85[ASN][1000 genomes]
rs11265607	0.94[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs11265609	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11582424	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11585004	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12127600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17654071	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs4845617	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6427631	0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs6427641	0.82[CEU][hapmap]
rs7553271	0.86[EUR][1000 genomes]
rs952146	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9651054	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9662562	0.80[AMR][1000 genomes]
rs9724691	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6427627	C1orf43	cis	parietal	SCAN
rs6427627	IL6R	Cis_1M	lymphoblastoid	RTeQTL
rs6427627	IL6R	cis	lymphoblastoid	seeQTL
rs6427627	PIP5K1A	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154326800-154360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:154357200-154359400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:154357400-154359200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:154357400-154359600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:154357400-154359600	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:154357400-154359600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:154357400-154359600	Enhancers	Fetal Thymus	thymus
8	chr1:154357600-154359600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:154357800-154359200	Weak transcription	Right Atrium	heart
10	chr1:154357800-154359800	Flanking Active TSS	HepG2	liver
11	chr1:154358000-154359200	Weak transcription	Liver	Liver
12	chr1:154358000-154359200	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr1:154358000-154359600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:154358200-154359200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:154358400-154359400	Weak transcription	GM12878-XiMat	blood
16	chr1:154358400-154359600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:154358400-154360400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:154358400-154362800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:154358400-154363600	Weak transcription	Esophagus	oesophagus
20	chr1:154358600-154359400	Weak transcription	Placenta	Placenta
21	chr1:154358600-154359600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:154358600-154363400	Weak transcription	NHEK	skin
23	chr1:154358600-154363600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:154358600-154364000	Weak transcription	Hela-S3	cervix
25	chr1:154358800-154359400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:154358800-154359400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:154358800-154359600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:154358800-154359600	Enhancers	Stomach Mucosa	stomach
29	chr1:154358800-154359600	Flanking Active TSS	K562	blood
30	chr1:154359000-154359200	Enhancers	Colonic Mucosa	Colon
31	chr1:154359000-154359600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr1:154359000-154359600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr1:154359000-154359600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:154359000-154359600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr1:154359000-154359600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr1:154359000-154359600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr1:154359000-154359600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr1:154359000-154359600	Enhancers	Lung	lung
39	chr1:154359000-154359600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:154359000-154359600	Enhancers	Thymus	Thymus
41	chr1:154359000-154360000	Enhancers	Primary T cells from cord blood	blood

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