Variant report

Variant	rs3110454
Chromosome Location	chr17:28651363-28651364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:28438776..28441159-chr17:28651258..28653956,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1050565	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs11656408	0.85[ASN][1000 genomes]
rs11867581	0.82[JPT][hapmap]
rs12938714	0.87[ASN][1000 genomes]
rs12939390	0.93[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12941223	0.87[ASN][1000 genomes]
rs12949747	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs13341611	0.82[JPT][hapmap]
rs1487971	0.82[JPT][hapmap]
rs17767256	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs2321706	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3103303	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3103306	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3110060	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110061	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110452	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33980254	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs34353378	0.85[ASN][1000 genomes]
rs34622227	0.87[ASN][1000 genomes]
rs35724800	0.81[ASN][1000 genomes]
rs36000555	0.87[ASN][1000 genomes]
rs36048853	0.91[ASN][1000 genomes]
rs3764449	0.93[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs3794806	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs3816828	0.88[JPT][hapmap]
rs6505165	0.82[JPT][hapmap]
rs6505169	0.82[JPT][hapmap]
rs6505173	0.82[JPT][hapmap]
rs7208052	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7210085	0.82[JPT][hapmap]
rs7214014	0.82[JPT][hapmap]
rs7214248	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs7214991	0.82[JPT][hapmap]
rs7215330	0.82[JPT][hapmap]
rs7223821	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs7342921	0.93[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7342929	0.82[JPT][hapmap]
rs8072345	0.82[JPT][hapmap]
rs8080149	0.85[ASN][1000 genomes]
rs998087	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1064975	chr17:28604187-28851905	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv543299	chr17:28604187-28851905	Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv543300	chr17:28620420-28659310	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3110454	CPD	cis	parietal	SCAN
rs3110454	GOSR1	cis	parietal	SCAN
rs3110454	BLMH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28639800-28653800	Weak transcription	Fetal Intestine Large	intestine
2	chr17:28644000-28667000	Weak transcription	Colonic Mucosa	Colon
3	chr17:28644200-28672600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:28644400-28658400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr17:28645600-28653800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr17:28648000-28663800	Weak transcription	Spleen	Spleen
7	chr17:28649000-28652200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr17:28649200-28651800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr17:28649200-28653800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:28649800-28651600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr17:28649800-28651800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr17:28649800-28651800	Enhancers	GM12878-XiMat	blood
13	chr17:28649800-28653800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:28650000-28651400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr17:28650000-28651400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:28650000-28651400	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr17:28650000-28651800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr17:28650000-28651800	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr17:28650000-28651800	Enhancers	Dnd41	blood
20	chr17:28650000-28652800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr17:28650200-28651400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr17:28650200-28651600	Enhancers	Thymus	Thymus
23	chr17:28650200-28651800	Bivalent Enhancer	NHEK	skin
24	chr17:28650400-28652200	Enhancers	K562	blood
25	chr17:28650400-28652600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:28650600-28651800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:28650600-28652400	Enhancers	HepG2	liver
28	chr17:28650800-28651400	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:28650800-28651600	Enhancers	Primary hematopoietic stem cells	blood
30	chr17:28650800-28652000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr17:28651000-28651600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr17:28651000-28652200	Enhancers	Primary T cells from cord blood	blood
33	chr17:28651000-28652400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr17:28651000-28657800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:28651200-28653000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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