Variant report

Variant	rs4102203
Chromosome Location	chr12:120976371-120976372
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RXRA	chr12:120976314-120976822	SK-N-SH	brain:	n/a	chr12:120976559-120976575
2	RCOR1	chr12:120975520-120977758	IMR90	lung:	n/a	n/a
3	SP1	chr12:120976314-120976747	HepG2	liver:	n/a	n/a
4	EP300	chr12:120976251-120976767	HepG2	liver:	n/a	n/a
5	SRF	chr12:120976369-120976599	HepG2	liver:	n/a	chr12:120976476-120976494
6	EP300	chr12:120976358-120976659	SK-N-SH_RA	brain:	n/a	n/a
7	HNF4G	chr12:120976333-120976665	HepG2	liver:	n/a	chr12:120976497-120976512 chr12:120976498-120976510 chr12:120976497-120976510
8	NFIC	chr12:120976348-120976817	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr12:120976322-120976804	SK-N-SH	brain:	n/a	n/a
10	RXRA	chr12:120976170-120976943	SK-N-SH	brain:	n/a	chr12:120976559-120976575
11	POLR2A	chr12:120976292-120976731	PANC-1	pancreas:	n/a	n/a
12	NFIC	chr12:120976194-120976973	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr12:120976244-120977624	SK-N-SH	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120975914..120977985-chr12:120980221..120984340,3	K562	blood:
2	chr12:120934821..120937142-chr12:120975702..120977289,2	K562	blood:
3	chr12:120904864..120906819-chr12:120975505..120978250,2	K562	blood:
4	chr12:120965545..120968418-chr12:120976359..120978449,2	K562	blood:
5	chr12:120974713..120977550-chr12:122230607..122232618,2	MCF-7	breast:
6	chr12:120932415..120934356-chr12:120975182..120977276,3	K562	blood:
7	chr12:120974437..120977304-chr12:120987855..120989624,2	K562	blood:
8	chr12:120971037..120975304-chr12:120975944..120978550,4	MCF-7	breast:
9	chr12:120974815..120979080-chr12:120980221..120984438,7	K562	blood:
10	chr12:120932415..120935413-chr12:120975182..120978134,3	K562	blood:
11	chr12:120965752..120968769-chr12:120974337..120978260,3	MCF-7	breast:

No data

Variant related genes	Relation type
COQ5	TF binding region
ENSG00000248008	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000110871	Chromatin interaction
ENSG00000022840	Chromatin interaction
ENSG00000088986	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10789	0.86[CEU][hapmap]
rs11065140	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs11065142	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs11548262	0.96[EUR][1000 genomes]
rs11608416	1.00[CEU][hapmap]
rs11608807	0.86[EUR][1000 genomes]
rs11609119	0.94[EUR][1000 genomes]
rs11611781	0.84[EUR][1000 genomes]
rs11611814	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11612519	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11613214	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs11614224	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11615264	1.00[EUR][1000 genomes]
rs11615719	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11829765	0.96[EUR][1000 genomes]
rs16950293	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2280168	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3742049	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs3759402	0.84[EUR][1000 genomes]
rs3817301	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3829291	0.85[EUR][1000 genomes]
rs4439575	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57646360	0.94[EUR][1000 genomes]
rs59088579	0.96[EUR][1000 genomes]
rs59201986	0.97[EUR][1000 genomes]
rs60162888	0.96[EUR][1000 genomes]
rs6490292	0.96[EUR][1000 genomes]
rs7027	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs7134710	0.94[EUR][1000 genomes]
rs719449	0.95[EUR][1000 genomes]
rs719450	1.00[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs7296473	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7297861	0.81[EUR][1000 genomes]
rs7299954	0.96[EUR][1000 genomes]
rs7314103	0.96[EUR][1000 genomes]
rs73403923	0.88[EUR][1000 genomes]
rs73403943	0.96[EUR][1000 genomes]
rs73403947	0.96[EUR][1000 genomes]
rs73403968	0.97[EUR][1000 genomes]
rs73403975	1.00[EUR][1000 genomes]
rs73405628	0.81[EUR][1000 genomes]
rs7961895	0.90[EUR][1000 genomes]
rs7962410	0.91[EUR][1000 genomes]
rs7964008	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs7973555	1.00[CEU][hapmap];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906	chr12:120973683-121018441	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4102203	GATC	cis	parietal	SCAN
rs4102203	GATC	cis	cerebellum	SCAN
rs4102203	POP5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120972800-120977400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:120972800-120977600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:120973000-120977200	Flanking Active TSS	Rectal Smooth Muscle	rectum
4	chr12:120973000-120977400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:120973000-120980200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:120973200-120977000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr12:120973200-120977000	Flanking Active TSS	Brain Angular Gyrus	brain
8	chr12:120973200-120977400	Flanking Active TSS	HUVEC	blood vessel
9	chr12:120973400-120976800	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr12:120973400-120984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:120973600-120976400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr12:120973600-120976600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:120973800-120984000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:120974000-120976600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:120974000-120977200	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr12:120974000-120977800	Enhancers	Spleen	Spleen
17	chr12:120974200-120976800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:120974200-120976800	Flanking Active TSS	HepG2	liver
19	chr12:120974200-120978600	Genic enhancers	Fetal Muscle Leg	muscle
20	chr12:120974400-120976600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:120974400-120976600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:120974400-120977400	Genic enhancers	Fetal Thymus	thymus
23	chr12:120974400-120977600	Enhancers	Stomach Mucosa	stomach
24	chr12:120974400-120977600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr12:120974400-120984200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:120974600-120976600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:120974600-120976600	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr12:120974600-120976800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:120974600-120976800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr12:120974600-120977400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:120974600-120977400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:120974600-120978600	Genic enhancers	Fetal Intestine Small	intestine
33	chr12:120974600-120979000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:120974600-120979400	Genic enhancers	K562	blood
35	chr12:120974600-120984000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:120974800-120976400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr12:120974800-120976600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:120974800-120977000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
39	chr12:120974800-120977400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:120974800-120977400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr12:120974800-120977400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr12:120974800-120978200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr12:120975000-120976400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:120975000-120976400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:120975000-120977400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr12:120975200-120976400	Weak transcription	Esophagus	oesophagus
47	chr12:120975200-120976800	Genic enhancers	Thymus	Thymus
48	chr12:120975200-120980000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:120975200-120982400	Enhancers	Pancreas	Pancrea
50	chr12:120975200-120985200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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