Variant report

Variant	rs2276566
Chromosome Location	chr2:234395159-234395160
allele	C/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	SP1	chr2:234395070-234397505	A549	lung:	n/a	chr2:234395462-234395471 chr2:234395461-234395473 chr2:234395458-234395472 chr2:234395461-234395473
2	POLR2A	chr2:234395004-234395251	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr2:234394997-234395307	HUVEC	blood vessel:	n/a	n/a
4	GATA3	chr2:234394758-234397682	A549	lung:	n/a	chr2:234395229-234395245 chr2:234395234-234395241 chr2:234395227-234395248 chr2:234395234-234395241 chr2:234395234-234395244 chr2:234395234-234395241 chr2:234397643-234397653
5	REST	chr2:234395076-234396694	A549	lung:	n/a	chr2:234395472-234395485
6	EP300	chr2:234394935-234397537	A549	lung:	n/a	n/a
7	BCL3	chr2:234394913-234396277	A549	lung:	n/a	n/a
8	MAX	chr2:234394664-234397748	A549	lung:	n/a	chr2:234394668-234394681 chr2:234394669-234394679 chr2:234394669-234394679 chr2:234394668-234394681 chr2:234394669-234394680 chr2:234394671-234394680 chr2:234394665-234394684 chr2:234394666-234394681 chr2:234394669-234394680 chr2:234394670-234394680 chr2:234394668-234394683 chr2:234394669-234394678 chr2:234394668-234394681 chr2:234394669-234394680 chr2:234394670-234394679
9	SP1	chr2:234394925-234396972	A549	lung:	n/a	chr2:234395462-234395471 chr2:234395461-234395473 chr2:234395458-234395472 chr2:234395461-234395473
10	POLR2A	chr2:234394452-234395981	A549	lung:	n/a	n/a
11	GATA3	chr2:234395007-234397664	SK-N-SH	brain:	n/a	chr2:234395229-234395245 chr2:234395234-234395241 chr2:234395227-234395248 chr2:234395234-234395241 chr2:234395234-234395244 chr2:234395234-234395241 chr2:234397643-234397653
12	SIX5	chr2:234394871-234396635	A549	lung:	n/a	n/a
13	JUND	chr2:234394967-234396387	SK-N-SH	brain:	n/a	chr2:234395890-234395901
14	MAX	chr2:234394893-234396767	A549	lung:	n/a	n/a
15	TCF12	chr2:234394776-234397500	A549	lung:	n/a	chr2:234395469-234395479 chr2:234394972-234394979
16	MYC	chr2:234395052-234395250	HUVEC	blood vessel:	n/a	n/a
17	GATA2	chr2:234394994-234396258	HUVEC	blood vessel:	n/a	chr2:234395229-234395245 chr2:234395234-234395241 chr2:234395227-234395248 chr2:234395234-234395241 chr2:234395234-234395244 chr2:234395234-234395241
18	EP300	chr2:234395139-234397461	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234393460..234398388-chr2:234612624..234620814,16	MCF-7	breast:
2	chr2:234357885..234360671-chr2:234393955..234395750,2	MCF-7	breast:
3	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
4	chr2:234394199..234396835-chr2:234450285..234452802,2	MCF-7	breast:
5	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
6	chr2:234393753..234400835-chr2:234472864..234476478,8	MCF-7	breast:
7	chr2:234389632..234392009-chr2:234393676..234396865,6	MCF-7	breast:
8	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:
9	chr2:234386214..234389809-chr2:234395089..234397205,3	MCF-7	breast:

Variant related genes	Relation type
USP40	TF binding region
ENSG00000224814	Chromatin interaction
ENSG00000167165	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10175828	0.89[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13016839	0.80[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13028688	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34013402	1.00[EUR][1000 genomes]
rs60064064	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs71421697	0.81[AMR][1000 genomes]
rs71421698	0.91[AMR][1000 genomes];0.82[EUR][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:118 , 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	chr2:234377800-234397200	Weak transcription	Small Intestine	intestine
7	chr2:234381600-234399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:234383400-234395400	Strong transcription	Brain Hippocampus Middle	brain
9	chr2:234383400-234400200	Strong transcription	Fetal Intestine Small	intestine
10	chr2:234384000-234395200	Strong transcription	Liver	Liver
11	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
12	chr2:234384400-234398200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:234384400-234402200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:234384400-234402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:234384600-234408400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr2:234386000-234397600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:234386600-234400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:234386800-234407800	Strong transcription	Fetal Intestine Large	intestine
19	chr2:234387200-234396600	Weak transcription	Psoas Muscle	Psoas
20	chr2:234387400-234402800	Strong transcription	Adipose Nuclei	Adipose
21	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:234387600-234396400	Weak transcription	Primary B cells from cord blood	blood
23	chr2:234388200-234402000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:234388400-234401800	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr2:234388600-234396600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:234389200-234395400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:234389800-234395400	Strong transcription	Brain Substantia Nigra	brain
28	chr2:234389800-234396800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:234389800-234398200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:234390200-234402800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:234390400-234395200	Strong transcription	Dnd41	blood
32	chr2:234390800-234395400	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
34	chr2:234391200-234404400	Strong transcription	Fetal Stomach	stomach
35	chr2:234391400-234402600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:234391600-234396400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:234391600-234397200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:234391600-234412000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:234391800-234398000	Strong transcription	Brain Anterior Caudate	brain
40	chr2:234392000-234411600	Weak transcription	Fetal Brain Female	brain
41	chr2:234392200-234402400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:234392400-234399400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:234392400-234403000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:234392800-234395400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:234392800-234397000	Weak transcription	Thymus	Thymus
46	chr2:234392800-234398200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:234392800-234406400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:234393000-234400800	Weak transcription	GM12878-XiMat	blood
49	chr2:234393000-234402400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:234393400-234395200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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