Variant report

Variant	rs33623
Chromosome Location	chr16:12007435-12007436
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:11886565..11889362-chr16:12006902..12008695,2	K562	blood:
2	chr16:11942158..11945019-chr16:12007276..12009748,2	K562	blood:
3	chr16:11941713..11946689-chr16:12006948..12011249,6	MCF-7	breast:
4	chr16:12006532..12011371-chr16:12068460..12073371,6	K562	blood:
5	chr16:11988764..11995180-chr16:12006980..12012068,9	MCF-7	breast:
6	chr16:11831944..11836692-chr16:12007199..12011492,4	K562	blood:
7	chr16:12006809..12011472-chr16:12069677..12072698,7	MCF-7	breast:
8	chr16:11988100..11996073-chr16:12007143..12011577,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260488	Chromatin interaction
ENSG00000262420	Chromatin interaction
ENSG00000263307	Chromatin interaction
ENSG00000171490	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000234719	Chromatin interaction
ENSG00000153066	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10852344	0.80[MEX][hapmap]
rs11075030	0.81[CHD][hapmap];0.80[MEX][hapmap]
rs11075032	0.80[MEX][hapmap]
rs11570136	0.80[CEU][hapmap]
rs11646545	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs11647818	0.81[ASN][1000 genomes]
rs12925740	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs153025	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs154148	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs171656	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs190461	0.85[EUR][1000 genomes]
rs2018199	0.88[CEU][hapmap]
rs2075158	0.88[CEU][hapmap]
rs251723	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28279	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33620	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33621	0.85[EUR][1000 genomes]
rs33624	0.85[EUR][1000 genomes]
rs33629	0.82[EUR][1000 genomes]
rs33631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33635	0.88[CEU][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs33637	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33639	0.86[ASW][hapmap];0.84[CHD][hapmap];0.80[MEX][hapmap]
rs33640	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33643	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33645	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33647	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33649	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33651	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33652	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33653	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33659	0.93[ASW][hapmap];0.80[MEX][hapmap]
rs33660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3850997	0.82[TSI][hapmap]
rs40311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4493057	0.80[CEU][hapmap]
rs4511557	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs456325	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs718081	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs7198817	0.92[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs7202234	0.92[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs8046617	0.83[ASN][1000 genomes]
rs8047726	0.81[ASN][1000 genomes]
rs8059891	0.84[CEU][hapmap]
rs8061189	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1735	chr16:11986963-12031597	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv974848	chr16:12005053-12020022	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs33623	TNFRSF17	cis	cerebellum	SCAN
rs33623	RSL1D1	cis	parietal	SCAN
rs33623	GSPT1	Cis_1M	lymphoblastoid	RTeQTL
rs33623	TNFRSF17	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11987800-12007600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:11987800-12008400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:11999800-12008000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr16:12002000-12008200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:12005400-12007800	Weak transcription	Ovary	ovary
6	chr16:12006000-12007600	Enhancers	Fetal Lung	lung
7	chr16:12006200-12007600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr16:12006200-12007600	Enhancers	Fetal Brain Male	brain
9	chr16:12006200-12007600	Enhancers	Fetal Heart	heart
10	chr16:12006200-12007800	Enhancers	Small Intestine	intestine
11	chr16:12006200-12008000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr16:12006200-12008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr16:12006200-12008600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:12006200-12008600	Transcr. at gene 5' and 3'	K562	blood
15	chr16:12006400-12008000	Enhancers	Stomach Mucosa	stomach
16	chr16:12006600-12007600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr16:12006600-12008600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr16:12006600-12010400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr16:12006800-12007600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr16:12006800-12007600	Enhancers	Primary B cells from peripheral blood	blood
21	chr16:12006800-12007600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr16:12006800-12007800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr16:12006800-12007800	Enhancers	Fetal Stomach	stomach
24	chr16:12006800-12008000	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr16:12006800-12008000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr16:12006800-12008000	Enhancers	Spleen	Spleen
27	chr16:12006800-12008200	Transcr. at gene 5' and 3'	Dnd41	blood
28	chr16:12006800-12008400	Flanking Active TSS	Osteobl	bone
29	chr16:12006800-12008600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr16:12006800-12008600	Flanking Active TSS	HUVEC	blood vessel
31	chr16:12006800-12009000	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr16:12007000-12007600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr16:12007000-12007800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr16:12007000-12008000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr16:12007000-12008200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr16:12007000-12008400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr16:12007000-12008400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr16:12007000-12008600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr16:12007000-12008600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr16:12007000-12009000	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr16:12007200-12007600	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr16:12007200-12007600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
43	chr16:12007200-12007600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
44	chr16:12007200-12007600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr16:12007200-12007600	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr16:12007200-12007800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr16:12007200-12007800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr16:12007200-12007800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr16:12007200-12007800	Flanking Active TSS	Colonic Mucosa	Colon
50	chr16:12007200-12007800	Enhancers	Fetal Muscle Leg	muscle

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