Variant report

Variant	rs73997630
Chromosome Location	chr2:234400882-234400883
allele	A/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	STAT3	chr2:234400788-234401185	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr2:234400758-234401053	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr2:234400767-234401124	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr2:234400832-234401788	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr2:234400711-234401873	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr2:234400677-234401722	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr2:234400789-234401824	MCF10A-Er-Src	breast:	n/a	chr2:234401593-234401604
8	STAT3	chr2:234400817-234401966	MCF10A-Er-Src	breast:	n/a	chr2:234401593-234401604
9	CEBPB	chr2:234400879-234401079	A549	lung:	n/a	n/a
10	FOS	chr2:234400711-234401965	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr2:234400848-234401174	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr2:234400742-234401773	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234400872..234402381-chr2:234473582..234476254,2	MCF-7	breast:
2	chr2:234395375..234398231-chr2:234399551..234402111,5	MCF-7	breast:
3	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:
4	chr2:234400113..234401794-chr2:234403565..234406076,3	MCF-7	breast:
5	chr2:234400105..234405009-chr2:234616033..234619892,4	MCF-7	breast:

Variant related genes	Relation type
USP40	TF binding region
ENSG00000167165	Chromatin interaction
ENSG00000224814	Chromatin interaction
ENSG00000085982	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]
rs73997631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997633	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:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
7	chr2:234384400-234402200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr2:234384400-234402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:234384600-234408400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr2:234386800-234407800	Strong transcription	Fetal Intestine Large	intestine
11	chr2:234387400-234402800	Strong transcription	Adipose Nuclei	Adipose
12	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:234388200-234402000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:234388400-234401800	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr2:234390200-234402800	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
17	chr2:234391200-234404400	Strong transcription	Fetal Stomach	stomach
18	chr2:234391400-234402600	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:234391600-234412000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:234392000-234411600	Weak transcription	Fetal Brain Female	brain
21	chr2:234392200-234402400	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:234392400-234403000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:234392800-234406400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:234393000-234402400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:234393600-234401000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:234393800-234403200	Strong transcription	Primary T cells from cord blood	blood
27	chr2:234394000-234403200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:234394200-234402600	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:234394400-234401000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:234395200-234406000	Weak transcription	Fetal Kidney	kidney
31	chr2:234395400-234404200	Weak transcription	Stomach Mucosa	stomach
32	chr2:234395600-234402200	Strong transcription	Left Ventricle	heart
33	chr2:234395600-234402600	Strong transcription	Right Ventricle	heart
34	chr2:234395600-234404800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:234395600-234431800	Weak transcription	Colonic Mucosa	Colon
36	chr2:234395800-234401600	Weak transcription	Aorta	Aorta
37	chr2:234395800-234402000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:234395800-234408000	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:234395800-234411400	Strong transcription	Liver	Liver
40	chr2:234396000-234407000	Strong transcription	HepG2	liver
41	chr2:234396400-234402000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr2:234396400-234402600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr2:234396400-234407600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr2:234396600-234406000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:234396800-234401200	Genic enhancers	A549	lung
46	chr2:234396800-234409600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:234397000-234401000	Weak transcription	NHLF	lung
48	chr2:234397000-234401600	Strong transcription	Colon Smooth Muscle	Colon
49	chr2:234397200-234402200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:234397200-234402600	Strong transcription	Lung	lung

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