Variant report

Variant	rs6744797
Chromosome Location	chr2:39996160-39996161
allele	C/T
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	POLR2A	chr2:39996085-39996285	K562	blood:	n/a	n/a
2	POLR2A	chr2:39996061-39996299	K562	blood:	n/a	n/a
3	GATA3	chr2:39996000-39996182	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr2:39995835-39996275	K562	blood:	n/a	n/a
5	POLR2A	chr2:39995876-39996194	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39996045..39997746-chr3:50647710..50649775,2	MCF-7	breast:

Variant related genes	Relation type
THUMPD2	TF binding region
ENSG00000114738	Chromatin interaction
ENSG00000114737	Chromatin interaction

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

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

rs_ID	r²[population]
rs10168666	1.00[AMR][1000 genomes]
rs10171615	1.00[AMR][1000 genomes]
rs10177342	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197101	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12712654	0.86[AFR][1000 genomes]
rs12712655	0.86[AFR][1000 genomes]
rs13393172	0.86[AFR][1000 genomes]
rs13412186	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416764	1.00[AMR][1000 genomes]
rs28406334	0.98[AFR][1000 genomes]
rs57728145	0.95[AFR][1000 genomes]
rs59146573	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61706206	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544243	0.94[AFR][1000 genomes]
rs6725034	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749057	0.84[AFR][1000 genomes]
rs6761738	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924903	1.00[AMR][1000 genomes]
rs7564579	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7603886	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
5	chr2:39971600-39998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:39972400-39998600	Strong transcription	HMEC	breast
7	chr2:39972400-39998800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:39973000-39998800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:39974200-39998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:39975000-39998400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:39975400-39997000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:39976200-39998800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:39976800-39999000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
16	chr2:39983000-39999200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:39983600-39996400	Strong transcription	NHDF-Ad	bronchial
18	chr2:39983600-39998600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:39983600-39999000	Strong transcription	HSMM	muscle
20	chr2:39984800-39999600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
22	chr2:39985200-39998400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:39985200-39999600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:39985200-39999600	Weak transcription	Psoas Muscle	Psoas
25	chr2:39985200-39999800	Weak transcription	Brain Substantia Nigra	brain
26	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
28	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:39985800-39996200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:39985800-39996200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:39985800-39996400	Weak transcription	Fetal Intestine Small	intestine
32	chr2:39985800-39999200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:39985800-39999400	Weak transcription	Aorta	Aorta
34	chr2:39985800-39999600	Weak transcription	Brain Angular Gyrus	brain
35	chr2:39985800-39999800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:39985800-39999800	Weak transcription	Small Intestine	intestine
37	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain
38	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:39985800-40005400	Weak transcription	Lung	lung
41	chr2:39986000-40004200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:39986200-40004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:39986800-39999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:39987400-39999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:39987400-39999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:39987400-39999800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:39987400-39999800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:39987400-40001000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:39987400-40001000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:39987600-40001000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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