Variant report

Variant	rs9909394
Chromosome Location	chr17:63160174-63160175
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:63151108..63154306-chr17:63159891..63162115,3	MCF-7	breast:
2	chr17:63160128..63162121-chr17:63168023..63170188,2	K562	blood:
3	chr17:63159589..63162697-chr17:63164587..63167490,3	K562	blood:
4	chr17:63158962..63160565-chr17:63168020..63170468,3	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12600391	0.83[CEU][hapmap]
rs1514500	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs1877822	0.83[CEU][hapmap]
rs2869580	0.81[CEU][hapmap]
rs4790954	0.81[CEU][hapmap]
rs8069964	0.83[CEU][hapmap]
rs8072603	0.81[CEU][hapmap]
rs9900252	0.82[CEU][hapmap]
rs9900568	0.81[CEU][hapmap]
rs9900709	0.81[CEU][hapmap]
rs9904540	0.93[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9909092	0.82[EUR][1000 genomes]
rs9914505	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9914790	0.81[CEU][hapmap]
rs9916373	0.81[CEU][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	nsv530764	chr17:62939944-63278472	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9909394	TBX2	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:63134400-63169000	Weak transcription	Colon Smooth Muscle	Colon
2	chr17:63141000-63175200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr17:63143600-63169400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr17:63145800-63167000	Weak transcription	Aorta	Aorta
5	chr17:63150200-63162800	Weak transcription	Fetal Stomach	stomach
6	chr17:63151800-63160200	Weak transcription	Spleen	Spleen
7	chr17:63153600-63175400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr17:63156000-63164400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr17:63156600-63165600	Weak transcription	Dnd41	blood
10	chr17:63157000-63179800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:63157200-63169600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:63159600-63160200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr17:63159600-63160400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:63159600-63160400	Enhancers	Duodenum Mucosa	Duodenum
15	chr17:63159600-63160400	Enhancers	Stomach Mucosa	stomach
16	chr17:63159600-63160800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:63159600-63161200	Enhancers	GM12878-XiMat	blood
18	chr17:63159600-63161600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:63159600-63162000	Enhancers	K562	blood
20	chr17:63159800-63160200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr17:63159800-63160400	Enhancers	Brain Anterior Caudate	brain
22	chr17:63159800-63160400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr17:63159800-63160400	Enhancers	A549	lung
24	chr17:63159800-63160400	Enhancers	NHLF	lung
25	chr17:63159800-63160600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr17:63159800-63160600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:63159800-63160600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:63159800-63160600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:63159800-63160600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:63159800-63160600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:63159800-63160600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr17:63159800-63160600	Enhancers	NHEK	skin
33	chr17:63159800-63160800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr17:63159800-63160800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:63159800-63160800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr17:63159800-63160800	Enhancers	Fetal Thymus	thymus
37	chr17:63159800-63161000	Enhancers	Primary hematopoietic stem cells	blood
38	chr17:63159800-63161400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr17:63159800-63162800	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr17:63160000-63160400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr17:63160000-63160400	Enhancers	Lung	lung
42	chr17:63160000-63160400	Enhancers	Thymus	Thymus
43	chr17:63160000-63160400	Flanking Active TSS	Hela-S3	cervix
44	chr17:63160000-63160400	Enhancers	HMEC	breast
45	chr17:63160000-63160400	Enhancers	NH-A	brain
46	chr17:63160000-63160600	Enhancers	Primary B cells from cord blood	blood
47	chr17:63160000-63160600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr17:63160000-63160600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr17:63160000-63160800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr17:63160000-63160800	Enhancers	HUES6 Cell Line	embryonic stem cell

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