Variant report

Variant	rs2361200
Chromosome Location	chr3:143541598-143541599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143540836..143543345-chr3:143547418..143549416,3	MCF-7	breast:
2	chr3:143534241..143536547-chr3:143539436..143542162,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10513219	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917152	0.82[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11918501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55654258	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62268880	0.83[EUR][1000 genomes]
rs62268900	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66585826	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6773298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6798159	1.00[CEU][hapmap];0.95[CHB][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67981921	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806661	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs72995501	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158100	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641634	0.87[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.88[TSI][hapmap];0.88[ASN][1000 genomes]
rs7641674	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1001076	chr3:143513526-143547076	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536747	chr3:143513526-143547076	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2361200	TFDP2	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143514200-143544200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143529600-143543800	Weak transcription	Stomach Mucosa	stomach
3	chr3:143531000-143543200	Weak transcription	NHDF-Ad	bronchial
4	chr3:143531800-143543200	Weak transcription	Aorta	Aorta
5	chr3:143533600-143543200	Weak transcription	Fetal Lung	lung
6	chr3:143533800-143543200	Weak transcription	Right Atrium	heart
7	chr3:143536000-143545200	Weak transcription	Gastric	stomach
8	chr3:143538000-143542200	Enhancers	Brain Substantia Nigra	brain
9	chr3:143538600-143542000	Enhancers	Brain Cingulate Gyrus	brain
10	chr3:143538800-143541800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:143539000-143542200	Enhancers	Brain Hippocampus Middle	brain
12	chr3:143539200-143544600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr3:143539400-143541800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:143539400-143541800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:143539400-143545000	Weak transcription	Liver	Liver
16	chr3:143539600-143541800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:143539600-143546600	Weak transcription	Esophagus	oesophagus
18	chr3:143539600-143550000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:143539800-143541600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr3:143539800-143541600	Enhancers	GM12878-XiMat	blood
21	chr3:143539800-143558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:143540000-143541800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:143540000-143543000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:143540000-143549600	Weak transcription	HSMM	muscle
25	chr3:143540200-143542200	Enhancers	Brain Anterior Caudate	brain
26	chr3:143540400-143542600	Enhancers	Adipose Nuclei	Adipose
27	chr3:143540600-143541600	Enhancers	Primary B cells from cord blood	blood
28	chr3:143540600-143541800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:143540600-143542200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:143540600-143542200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr3:143540600-143542400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:143540600-143542400	Enhancers	Fetal Muscle Leg	muscle
33	chr3:143540600-143543200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:143540800-143542000	Enhancers	Fetal Stomach	stomach
35	chr3:143540800-143542200	Enhancers	Rectal Smooth Muscle	rectum
36	chr3:143540800-143542400	Enhancers	Colon Smooth Muscle	Colon
37	chr3:143541000-143541800	Enhancers	Stomach Smooth Muscle	stomach
38	chr3:143541000-143542200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:143541000-143543400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:143541000-143554200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:143541200-143541600	Weak transcription	Brain Angular Gyrus	brain
42	chr3:143541200-143541600	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr3:143541200-143541800	Enhancers	Fetal Kidney	kidney
44	chr3:143541200-143541800	Weak transcription	HSMMtube	muscle
45	chr3:143541200-143543200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:143541200-143543400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:143541400-143543400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:143541400-143543600	Weak transcription	Dnd41	blood
49	chr3:143541400-143543600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr3:143541400-143544000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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