Variant report

Variant	rs2629768
Chromosome Location	chr12:104361176-104361177
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	HCFC1	chr12:104358419-104361266	Hela-S3	cervix:	n/a	n/a
2	ZNF384	chr12:104361153-104361200	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:104360943-104361196	SK-N-SH	brain:	n/a	n/a
4	BATF	chr12:104360891-104361285	GM12878	blood:	n/a	chr12:104361134-104361144 chr12:104361130-104361140
5	FOS	chr12:104360970-104361285	MCF10A-Er-Src	breast:	n/a	chr12:104361133-104361140 chr12:104361132-104361142 chr12:104361133-104361141 chr12:104361133-104361141 chr12:104361132-104361142
6	POLR2A	chr12:104360618-104361287	H1-hESC	embryonic stem cell:	n/a	n/a
7	BATF	chr12:104360964-104361220	GM12878	blood:	n/a	chr12:104361134-104361144 chr12:104361130-104361140
8	FOS	chr12:104360951-104361274	MCF10A-Er-Src	breast:	n/a	chr12:104361133-104361140 chr12:104361132-104361142 chr12:104361133-104361141 chr12:104361133-104361141 chr12:104361132-104361142
9	NFIC	chr12:104360805-104361267	GM12878	blood:	n/a	n/a
10	FOS	chr12:104361005-104361268	MCF10A-Er-Src	breast:	n/a	chr12:104361133-104361140 chr12:104361132-104361142 chr12:104361133-104361141 chr12:104361133-104361141 chr12:104361132-104361142

No.	Distal block	Cell Line	Cell type
1	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
2	chr12:104356409..104362053-chr12:104528975..104533138,7	MCF-7	breast:
3	chr12:104358555..104361363-chr12:104388778..104391446,2	MCF-7	breast:
4	chr12:104359553..104362361-chr12:104443780..104446717,2	K562	blood:
5	chr12:104360101..104362239-chr12:104530545..104532165,2	MCF-7	breast:
6	chr12:104323078..104325496-chr12:104361053..104362555,2	MCF-7	breast:
7	chr12:104233429..104235958-chr12:104358438..104361946,3	MCF-7	breast:
8	chr12:104361070..104362835-chr12:104394971..104397683,2	MCF-7	breast:
9	chr12:104359459..104362433-chr12:104679529..104682592,4	K562	blood:

Variant related genes	Relation type
C12orf73	TF binding region
ENSG00000257327	Chromatin interaction
ENSG00000120820	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000265072	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1165687	1.00[CHD][hapmap]
rs1177458	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12369815	1.00[JPT][hapmap]
rs172814	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1866074	0.88[LWK][hapmap]
rs2254063	0.82[EUR][1000 genomes]
rs2254064	0.86[GIH][hapmap];0.93[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2576973	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583227	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583251	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583260	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583261	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2583263	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583277	0.83[EUR][1000 genomes]
rs2629770	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2629771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2629779	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2629793	0.81[LWK][hapmap]
rs2629804	0.81[TSI][hapmap]
rs2700510	0.91[AFR][1000 genomes]
rs2722200	0.91[AFR][1000 genomes]
rs2723846	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723847	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs322102	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs322105	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322106	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322107	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322108	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322110	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs784081	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs796736	1.00[AFR][1000 genomes];0.98[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	esv3359723	chr12:104359646-104370785	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2629768	KRTHB5	Cis_1M	lymphoblastoid	RTeQTL
rs2629768	MYBPC1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104357800-104361200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:104358200-104361200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:104358400-104361200	Active TSS	Psoas Muscle	Psoas
4	chr12:104358600-104361200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:104358600-104361200	Active TSS	Fetal Intestine Small	intestine
6	chr12:104358600-104361200	Active TSS	Right Atrium	heart
7	chr12:104358600-104361400	Active TSS	HSMMtube	muscle
8	chr12:104358600-104361600	Active TSS	GM12878-XiMat	blood
9	chr12:104358600-104363600	Active TSS	Right Ventricle	heart
10	chr12:104358800-104361200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:104358800-104361200	Active TSS	Left Ventricle	heart
12	chr12:104358800-104361600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:104359000-104361600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr12:104360000-104361200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:104360200-104361200	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr12:104360200-104361200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr12:104360200-104361200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:104360200-104361600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:104360400-104361200	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr12:104360400-104361200	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr12:104360400-104361600	Weak transcription	Spleen	Spleen
22	chr12:104360400-104363200	Weak transcription	Gastric	stomach
23	chr12:104360400-104368000	Weak transcription	Pancreas	Pancrea
24	chr12:104360600-104361200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:104360600-104361200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:104360600-104361200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr12:104360600-104361200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:104360600-104361200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:104360600-104361200	Enhancers	Primary B cells from peripheral blood	blood
30	chr12:104360600-104361200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr12:104360600-104361200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr12:104360600-104361200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:104360600-104361200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:104360600-104361200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:104360600-104361200	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr12:104360600-104361200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr12:104360600-104361200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:104360600-104361200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr12:104360600-104361200	Flanking Active TSS	Fetal Brain Female	brain
40	chr12:104360600-104361200	Flanking Active TSS	Hela-S3	cervix
41	chr12:104360600-104361200	Flanking Active TSS	HUVEC	blood vessel
42	chr12:104360600-104361200	Flanking Active TSS	K562	blood
43	chr12:104360600-104361200	Flanking Active TSS	NH-A	brain
44	chr12:104360600-104361200	Flanking Active TSS	NHEK	skin
45	chr12:104360600-104361200	Flanking Active TSS	Osteobl	bone
46	chr12:104360600-104361400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr12:104360600-104361600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:104360600-104361600	Flanking Active TSS	Dnd41	blood
49	chr12:104360600-104362200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:104360600-104362600	Enhancers	Sigmoid Colon	Sigmoid Colon

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