Variant report

Variant	rs322106
Chromosome Location	chr12:104358651-104358652
allele	C/T
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	HCFC1	chr12:104358419-104361266	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:104358245-104360335	K562	blood:	n/a	n/a
3	POLR2A	chr12:104358597-104361078	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr12:104358618-104360631	A549	lung:	n/a	chr12:104359744-104359751 chr12:104359568-104359577 chr12:104358870-104358879 chr12:104359407-104359416 chr12:104359568-104359577
5	POLR2A	chr12:104358246-104360260	GM19099	blood:	n/a	n/a
6	RUNX3	chr12:104358537-104358980	GM12878	blood:	n/a	n/a
7	MAZ	chr12:104358383-104360788	IMR90	lung:	n/a	chr12:104359744-104359751 chr12:104359568-104359577 chr12:104358870-104358879 chr12:104359407-104359416 chr12:104359568-104359577
8	POLR2A	chr12:104358052-104360401	PFSK-1	brain:	n/a	n/a
9	USF2	chr12:104358623-104359811	Hela-S3	cervix:	n/a	chr12:104359568-104359577 chr12:104359566-104359577 chr12:104359568-104359577 chr12:104359566-104359579 chr12:104359569-104359578
10	POLR2A	chr12:104357794-104360395	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr12:104358195-104361110	GM12891	blood:	n/a	n/a
12	USF1	chr12:104358622-104358939	SK-N-SH_RA	brain:	n/a	chr12:104358758-104358769
13	REST	chr12:104358616-104360557	H1-neurons	neurons:	n/a	chr12:104360178-104360198 chr12:104359845-104359858 chr12:104359393-104359402
14	USF1	chr12:104358638-104358868	SK-N-SH_RA	brain:	n/a	chr12:104358758-104358769
15	BHLHE40	chr12:104358564-104360073	GM12878	blood:	n/a	chr12:104359568-104359577 chr12:104359568-104359577 chr12:104359566-104359579 chr12:104359569-104359578
16	USF1	chr12:104358558-104359020	K562	blood:	n/a	chr12:104358758-104358769
17	POLR2A	chr12:104358262-104360391	HUVEC	blood vessel:	n/a	n/a
18	USF2	chr12:104358613-104358869	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:104358599-104358925	K562	blood:	n/a	n/a
20	MXI1	chr12:104358636-104359061	GM12878	blood:	n/a	n/a
21	BHLHE40	chr12:104358564-104360191	K562	blood:	n/a	chr12:104359568-104359577 chr12:104359568-104359577 chr12:104359566-104359579 chr12:104359569-104359578
22	POLR2A	chr12:104358641-104360270	PBDE	blood:	n/a	n/a
23	USF1	chr12:104358608-104358890	K562	blood:	n/a	chr12:104358758-104358769
24	POLR2A	chr12:104358049-104358863	GM12892	blood:	n/a	n/a
25	USF1	chr12:104358639-104358880	HepG2	liver:	n/a	chr12:104358758-104358769
26	POLR2A	chr12:104358369-104360662	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr12:104358136-104360479	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr12:104358580-104360717	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr12:104358639-104360566	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr12:104358538-104360448	HUVEC	blood vessel:	n/a	n/a
31	ZNF263	chr12:104358584-104360162	HEK293-T-REx	kidney:	n/a	n/a
32	POLR2A	chr12:104358192-104360355	GM12878	blood:	n/a	n/a
33	BHLHE40	chr12:104358633-104358934	HepG2	liver:	n/a	n/a
34	POLR2A	chr12:104358565-104360341	PANC-1	pancreas:	n/a	n/a
35	USF1	chr12:104358571-104358921	SK-N-SH	brain:	n/a	chr12:104358758-104358769

No.	Distal block	Cell Line	Cell type
1	chr12:104358049..104359986-chr12:104530882..104532737,3	K562	blood:
2	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:
3	chr12:104357292..104359018-chr12:104494120..104496296,2	MCF-7	breast:
4	chr12:104357850..104359549-chr12:104531019..104533949,2	K562	blood:
5	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
6	chr12:104356409..104362053-chr12:104528975..104533138,7	MCF-7	breast:
7	chr12:104358555..104361363-chr12:104388778..104391446,2	MCF-7	breast:
8	chr12:104322943..104325215-chr12:104358408..104360868,4	MCF-7	breast:
9	chr12:104328917..104332179-chr12:104357230..104361045,4	MCF-7	breast:
10	chr12:104233429..104235958-chr12:104358438..104361946,3	MCF-7	breast:
11	chr12:102510855..102512497-chr12:104358534..104361115,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf73-2	chr12:104357568-104359481	NONHSAT030401

Variant related genes	Relation type
TDG	TF binding region
ENSG00000120820	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000075188	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000214198	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1177458	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs172814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254063	0.82[EUR][1000 genomes]
rs2254064	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2576973	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583227	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583251	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583260	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583261	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2583263	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583277	0.83[EUR][1000 genomes]
rs2629768	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2629770	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2629771	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2629779	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2700510	0.91[AFR][1000 genomes]
rs2722200	0.91[AFR][1000 genomes]
rs2723846	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723847	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723876	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs322102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs322105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322108	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322110	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs784081	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs796736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1799879	chr12:104351057-104360713	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs322106	KRTHB5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104357600-104359000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:104357800-104358800	Enhancers	Primary T cells fromperipheralblood	blood
3	chr12:104357800-104358800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:104357800-104358800	Flanking Active TSS	NHLF	lung
5	chr12:104357800-104359400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:104357800-104361200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:104358000-104358800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:104358000-104358800	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:104358000-104358800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:104358000-104358800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:104358000-104358800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:104358000-104358800	Enhancers	Left Ventricle	heart
13	chr12:104358000-104358800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr12:104358000-104359200	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr12:104358000-104359400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr12:104358000-104360600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:104358000-104360800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr12:104358200-104358800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:104358200-104358800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr12:104358200-104358800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr12:104358200-104358800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr12:104358200-104358800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:104358200-104358800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:104358200-104358800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr12:104358200-104358800	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr12:104358200-104358800	Enhancers	Placenta	Placenta
27	chr12:104358200-104358800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr12:104358200-104358800	Flanking Active TSS	Hela-S3	cervix
29	chr12:104358200-104358800	Flanking Active TSS	HMEC	breast
30	chr12:104358200-104358800	Flanking Active TSS	NHEK	skin
31	chr12:104358200-104359000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr12:104358200-104359000	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr12:104358200-104359000	Flanking Active TSS	Fetal Heart	heart
34	chr12:104358200-104359000	Flanking Active TSS	Dnd41	blood
35	chr12:104358200-104359200	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr12:104358200-104359200	Flanking Active TSS	NH-A	brain
37	chr12:104358200-104359400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:104358200-104359400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:104358200-104359400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr12:104358200-104360600	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr12:104358200-104360600	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr12:104358200-104361200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:104358400-104358800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:104358400-104358800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:104358400-104358800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:104358400-104358800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr12:104358400-104358800	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr12:104358400-104358800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:104358400-104358800	Flanking Active TSS	Fetal Lung	lung
50	chr12:104358400-104358800	Enhancers	Pancreas	Pancrea

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