Variant report

Variant	rs12122920
Chromosome Location	chr1:151588735-151588736
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	JUND	chr1:151588216-151588810	T-47D	breast:	n/a	chr1:151588295-151588307
2	TCF7L2	chr1:151588430-151589239	HEK293	kidney:	n/a	chr1:151588601-151588615 chr1:151588604-151588613 chr1:151588600-151588616 chr1:151588600-151588616 chr1:151588604-151588614 chr1:151588603-151588612 chr1:151588601-151588615
3	TCF7L2	chr1:151588536-151588798	HepG2	liver:	n/a	chr1:151588601-151588615 chr1:151588604-151588613 chr1:151588600-151588616 chr1:151588600-151588616 chr1:151588604-151588614 chr1:151588603-151588612 chr1:151588601-151588615
4	FOXA1	chr1:151588357-151588805	T-47D	breast:	n/a	n/a
5	EP300	chr1:151588277-151588926	T-47D	breast:	n/a	n/a
6	GATA3	chr1:151588273-151588794	T-47D	breast:	n/a	n/a
7	GATA3	chr1:151588319-151588795	T-47D	breast:	n/a	n/a
8	TCF7L2	chr1:151588449-151588787	PANC-1	pancreas:	n/a	chr1:151588601-151588615 chr1:151588604-151588613 chr1:151588600-151588616 chr1:151588600-151588616 chr1:151588604-151588614 chr1:151588603-151588612 chr1:151588601-151588615
9	TCF7L2	chr1:151588396-151588883	MCF-7	breast:	n/a	chr1:151588601-151588615 chr1:151588604-151588613 chr1:151588600-151588616 chr1:151588600-151588616 chr1:151588604-151588614 chr1:151588603-151588612 chr1:151588601-151588615
10	STAT3	chr1:151588571-151589130	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151484902..151486680-chr1:151588656..151591283,2	MCF-7	breast:
2	chr1:151588452..151590305-chr1:151592853..151595433,2	MCF-7	breast:
3	chr1:151580809..151584127-chr1:151586626..151590699,5	MCF-7	breast:
4	chr1:151585984..151590986-chr1:151591499..151594499,5	K562	blood:
5	chr1:151584561..151586532-chr1:151587199..151588882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250734	TF binding region
ENSG00000250734	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1048694	0.84[MEX][hapmap]
rs11808761	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs1196350	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196357	0.84[MEX][hapmap]
rs1196462	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1196466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1196468	0.85[ASN][1000 genomes]
rs1201651	0.84[MEX][hapmap]
rs1211981	0.84[MEX][hapmap]
rs12128050	0.84[ASN][1000 genomes]
rs12723676	0.84[ASN][1000 genomes]
rs1308145	0.84[MEX][hapmap]
rs1891589	0.84[MEX][hapmap]
rs2495392	0.84[MEX][hapmap]
rs3466	1.00[ASW][hapmap]
rs35086333	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818467	0.81[ASN][1000 genomes]
rs6587615	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs6587617	0.83[CHB][hapmap]
rs6696250	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs878775	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs939592	0.81[CEU][hapmap];0.83[TSI][hapmap]

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	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12122920	BCL9	cis	cerebellum	SCAN
rs12122920	LCE1C	cis	parietal	SCAN
rs12122920	TDRKH	cis	cerebellum	SCAN
rs12122920	LYSMD1	cis	parietal	SCAN
rs12122920	GATAD2B	cis	cerebellum	SCAN
rs12122920	FLG2	cis	cerebellum	SCAN
rs12122920	SNX27	cis	cerebellum	SCAN
rs12122920	SPRR2B	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151584600-151589600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:151586000-151589600	Enhancers	NHEK	skin
3	chr1:151586200-151591000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:151586200-151591600	Weak transcription	Gastric	stomach
5	chr1:151586200-151591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:151586200-151593200	Enhancers	HepG2	liver
7	chr1:151586400-151588800	Weak transcription	HSMM	muscle
8	chr1:151586400-151589000	Weak transcription	Small Intestine	intestine
9	chr1:151586400-151589600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:151586400-151589600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:151586400-151589600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:151586400-151590000	Weak transcription	Fetal Intestine Large	intestine
13	chr1:151586400-151590000	Weak transcription	Stomach Mucosa	stomach
14	chr1:151586400-151590200	Weak transcription	Fetal Intestine Small	intestine
15	chr1:151586400-151591400	Weak transcription	Placenta	Placenta
16	chr1:151586400-151591800	Weak transcription	Brain Substantia Nigra	brain
17	chr1:151586400-151592000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:151586400-151592200	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:151586400-151592200	Weak transcription	Fetal Stomach	stomach
20	chr1:151586400-151592200	Weak transcription	NHDF-Ad	bronchial
21	chr1:151586400-151592400	Weak transcription	Lung	lung
22	chr1:151586400-151593800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:151586400-151594200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:151586400-151600600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:151586400-151610200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:151586400-151610400	Weak transcription	Left Ventricle	heart
27	chr1:151586400-151611400	Weak transcription	Esophagus	oesophagus
28	chr1:151586400-151622200	Weak transcription	Fetal Thymus	thymus
29	chr1:151586400-151626600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:151586600-151589000	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr1:151586600-151589600	Genic enhancers	Dnd41	blood
32	chr1:151586600-151590000	Weak transcription	Liver	Liver
33	chr1:151586600-151591800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:151586600-151592000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:151586600-151592200	Weak transcription	Adipose Nuclei	Adipose
36	chr1:151586600-151592200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:151586600-151603000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:151586600-151605600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:151586800-151589400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:151586800-151589600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:151586800-151590600	Weak transcription	Fetal Kidney	kidney
42	chr1:151586800-151590800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:151586800-151590800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:151586800-151591000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:151586800-151591200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:151586800-151591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:151586800-151591200	Weak transcription	NHLF	lung
48	chr1:151586800-151591600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:151586800-151591600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:151586800-151591600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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