Variant report

Variant	rs17123927
Chromosome Location	chr12:50149347-50149348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50149134-50149422	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50134981..50136856-chr12:50149299..50151723,2	MCF-7	breast:
2	chr12:50146790..50149576-chr12:50162181..50164757,2	K562	blood:
3	chr12:50143917..50145697-chr12:50149068..50150668,2	MCF-7	breast:

Variant related genes	Relation type
TMBIM6	TF binding region
ENSG00000139644	Chromatin interaction
ENSG00000257730	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1012874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1049986	0.87[CEU][hapmap]
rs10506287	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506288	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169097	0.87[CEU][hapmap]
rs11169106	0.87[CEU][hapmap]
rs11169125	0.87[CEU][hapmap]
rs11169126	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169127	0.87[CEU][hapmap]
rs11169143	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830696	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834380	0.87[CEU][hapmap]
rs11836837	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837639	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299505	0.87[CEU][hapmap]
rs12306422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307828	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310510	0.86[CEU][hapmap]
rs12313353	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12313354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314795	1.00[CEU][hapmap]
rs12315524	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317778	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1317131	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470906	0.87[CEU][hapmap]
rs1574326	0.87[CEU][hapmap]
rs17123764	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123970	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993398	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303305	0.87[TSI][hapmap]
rs2336058	0.87[CEU][hapmap]
rs2336447	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563	0.87[CEU][hapmap]
rs4584654	0.87[CEU][hapmap]
rs4641552	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55637397	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56737983	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56743994	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56906356	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56945609	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57291131	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58756176	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59261129	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60094911	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60126713	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415769	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60613973	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61281663	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137976	0.87[CEU][hapmap]
rs7298080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74086911	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087113	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087134	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087188	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74089557	0.86[ASN][1000 genomes]
rs74089564	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089566	1.00[ASN][1000 genomes]
rs74089570	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089573	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487779	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7487854	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688	0.87[CEU][hapmap]
rs7952734	0.87[CEU][hapmap]
rs7953412	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964320	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967073	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7968302	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970674	0.87[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971369	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973498	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979262	0.85[CEU][hapmap]
rs9805063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17123927	USP35	trans	brain	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50137200-50152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:50137400-50150800	Weak transcription	Fetal Brain Male	brain
3	chr12:50144000-50151600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:50145000-50156000	Strong transcription	Dnd41	blood
5	chr12:50145000-50157000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:50145000-50159200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:50145200-50149600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
8	chr12:50145200-50149600	Strong transcription	Hela-S3	cervix
9	chr12:50145200-50149600	Strong transcription	K562	blood
10	chr12:50145200-50149600	Strong transcription	NHEK	skin
11	chr12:50145600-50149800	Strong transcription	HepG2	liver
12	chr12:50145800-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:50146000-50149600	Genic enhancers	Liver	Liver
14	chr12:50146000-50151000	Weak transcription	Stomach Mucosa	stomach
15	chr12:50146000-50157000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr12:50146000-50159000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:50146000-50159000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:50146000-50159000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:50146200-50149600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:50146200-50149600	Strong transcription	Fetal Kidney	kidney
21	chr12:50146200-50149600	Strong transcription	A549	lung
22	chr12:50146200-50150200	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr12:50146200-50154200	Strong transcription	Fetal Thymus	thymus
24	chr12:50146200-50155200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:50146200-50155800	Strong transcription	Primary T cells from cord blood	blood
26	chr12:50146200-50156000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr12:50146200-50156200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:50146200-50159000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:50146200-50159000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:50146200-50159000	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr12:50146200-50159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:50146200-50159200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:50146200-50159200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:50146200-50159200	Strong transcription	Placenta	Placenta
35	chr12:50146400-50155000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:50146400-50155000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:50146400-50155000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:50146400-50155200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:50146400-50156200	Strong transcription	HUVEC	blood vessel
40	chr12:50146400-50158200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:50146400-50158400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr12:50146400-50158400	Strong transcription	Fetal Lung	lung
43	chr12:50146400-50158400	Strong transcription	Ovary	ovary
44	chr12:50146400-50159000	Strong transcription	Brain Germinal Matrix	brain
45	chr12:50146400-50159200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:50146400-50159200	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr12:50146400-50159400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:50146400-50159400	Strong transcription	Fetal Brain Female	brain
49	chr12:50146400-50159600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr12:50146400-50159800	Strong transcription	Fetal Muscle Trunk	muscle

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