Variant report

Variant	rs73997633
Chromosome Location	chr2:234404860-234404861
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	POLR2A	chr2:234404852-234404968	K562	blood:	n/a	n/a
2	SP1	chr2:234404319-234405042	A549	lung:	n/a	n/a
3	EP300	chr2:234403975-234405135	A549	lung:	n/a	chr2:234404793-234404803
4	TCF12	chr2:234404243-234405050	A549	lung:	n/a	chr2:234404424-234404431 chr2:234404648-234404657 chr2:234404794-234404803

No.	Distal block	Cell Line	Cell type
1	chr2:234404504..234406876-chr2:234739242..234740869,2	MCF-7	breast:
2	chr2:234400113..234401794-chr2:234403565..234406076,3	MCF-7	breast:
3	chr2:234400105..234405009-chr2:234616033..234619892,4	MCF-7	breast:
4	chr2:234404472..234406274-chr2:234599019..234601933,2	MCF-7	breast:

Variant related genes	Relation type
USP40	TF binding region
ENSG00000167165	Chromatin interaction
ENSG00000224814	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs28968505	0.84[AFR][1000 genomes]
rs4047262	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4281901	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4392254	1.00[AMR][1000 genomes]
rs4588184	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55888324	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56274731	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56306918	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56317380	1.00[AMR][1000 genomes]
rs57285092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57768657	0.84[AFR][1000 genomes]
rs58330864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58489211	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58583213	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58864422	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59543173	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59954119	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61376069	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726032	1.00[AMR][1000 genomes]
rs6734355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995909	1.00[AMR][1000 genomes]
rs73995911	1.00[AMR][1000 genomes]
rs73995918	1.00[AMR][1000 genomes]
rs73995919	1.00[AMR][1000 genomes]
rs73995920	1.00[AMR][1000 genomes]
rs73995921	1.00[AMR][1000 genomes]
rs73995922	1.00[AMR][1000 genomes]
rs73995923	1.00[AMR][1000 genomes]
rs73995944	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995945	0.84[AFR][1000 genomes]
rs73995946	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995947	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995948	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995949	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995950	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995970	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995973	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995974	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995980	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996001	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996107	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996118	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996119	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996120	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996121	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996124	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996138	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997606	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997607	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997608	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997611	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997612	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs745154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7580191	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7584192	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7593807	1.00[AMR][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
5	chr2:234384600-234408400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:234386800-234407800	Strong transcription	Fetal Intestine Large	intestine
7	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
9	chr2:234391600-234412000	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:234392000-234411600	Weak transcription	Fetal Brain Female	brain
11	chr2:234392800-234406400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:234395200-234406000	Weak transcription	Fetal Kidney	kidney
13	chr2:234395600-234431800	Weak transcription	Colonic Mucosa	Colon
14	chr2:234395800-234408000	Strong transcription	Fetal Muscle Leg	muscle
15	chr2:234395800-234411400	Strong transcription	Liver	Liver
16	chr2:234396000-234407000	Strong transcription	HepG2	liver
17	chr2:234396400-234407600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr2:234396600-234406000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:234396800-234409600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:234397800-234411400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:234398000-234406000	Weak transcription	Primary B cells from cord blood	blood
22	chr2:234398000-234452800	Weak transcription	HUVEC	blood vessel
23	chr2:234398200-234405800	Weak transcription	Brain Germinal Matrix	brain
24	chr2:234398200-234411200	Weak transcription	Esophagus	oesophagus
25	chr2:234398200-234411200	Weak transcription	Thymus	Thymus
26	chr2:234398400-234442400	Weak transcription	Hela-S3	cervix
27	chr2:234398600-234406600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:234398600-234408800	Weak transcription	NH-A	brain
29	chr2:234398600-234431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:234398800-234407600	Strong transcription	HSMM	muscle
31	chr2:234398800-234408800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:234399000-234406200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:234399000-234408400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:234399000-234408400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:234399000-234409000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:234399000-234409200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:234399200-234405200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:234399600-234410000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:234400200-234406200	Weak transcription	HSMMtube	muscle
40	chr2:234400200-234410600	Weak transcription	Small Intestine	intestine
41	chr2:234400400-234430000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:234400800-234406400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:234401200-234407200	Weak transcription	Fetal Lung	lung
44	chr2:234401200-234410400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:234401200-234411200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:234401200-234430800	Weak transcription	NHLF	lung
47	chr2:234401600-234406000	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:234401800-234405800	Weak transcription	Aorta	Aorta
49	chr2:234401800-234410400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:234402000-234406000	Weak transcription	Primary monocytes fromperipheralblood	blood

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