Variant report

Variant	rs6742533
Chromosome Location	chr2:39976624-39976625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10168666	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10171615	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10177342	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197101	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12712654	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs12712655	0.99[AFR][1000 genomes]
rs13393172	0.91[ASW][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs13412186	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416764	1.00[AMR][1000 genomes]
rs28406334	0.85[AFR][1000 genomes]
rs57728145	0.82[AFR][1000 genomes]
rs59146573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61706206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544243	0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs6725034	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6744797	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749057	0.91[ASW][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6761738	0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924903	1.00[AMR][1000 genomes]
rs7564579	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7603886	1.00[AMR][1000 genomes]
rs7604790	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:39960400-39983000	Weak transcription	Stomach Mucosa	stomach
3	chr2:39961400-39984200	Weak transcription	Colonic Mucosa	Colon
4	chr2:39962200-39986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:39962200-39993200	Strong transcription	Liver	Liver
6	chr2:39962800-39980200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:39963200-39982000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:39964000-39976800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:39964200-39976800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:39964200-39977000	Weak transcription	Brain Angular Gyrus	brain
11	chr2:39964200-39977400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:39964200-39984200	Weak transcription	Psoas Muscle	Psoas
13	chr2:39964400-39977000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:39964800-39983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:39965200-39980000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:39965200-39983000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:39965400-39984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:39966600-39976800	Weak transcription	Small Intestine	intestine
21	chr2:39966800-39980000	Weak transcription	Esophagus	oesophagus
22	chr2:39966800-39980200	Weak transcription	Lung	lung
23	chr2:39966800-39983200	Weak transcription	Spleen	Spleen
24	chr2:39967000-39976800	Weak transcription	Gastric	stomach
25	chr2:39967000-39981000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:39967000-39983000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:39967000-39983200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:39967000-39983400	Weak transcription	Aorta	Aorta
29	chr2:39967200-39983000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:39967600-39976800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:39967600-39991200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:39970000-39976800	Weak transcription	HSMMtube	muscle
34	chr2:39970200-39978200	Weak transcription	GM12878-XiMat	blood
35	chr2:39970800-39976800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:39970800-39983000	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:39971000-39976800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:39971000-39976800	Weak transcription	Ovary	ovary
39	chr2:39971000-39976800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:39971000-39976800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:39971000-39980000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:39971000-39980000	Weak transcription	Left Ventricle	heart
43	chr2:39971000-39983000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:39971000-39983000	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
46	chr2:39971200-39976800	Weak transcription	Dnd41	blood
47	chr2:39971200-39978600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr2:39971400-39977000	Weak transcription	NHDF-Ad	bronchial
49	chr2:39971400-39982400	Strong transcription	HSMM	muscle
50	chr2:39971600-39981000	Weak transcription	HUVEC	blood vessel

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