Variant report

Variant	rs1130609
Chromosome Location	chr2:10262920-10262921
allele	G/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	SP1	chr2:10260054-10263386	A549	lung:	n/a	chr2:10260485-10260497 chr2:10262403-10262412 chr2:10260481-10260490 chr2:10262398-10262412 chr2:10260439-10260448 chr2:10262401-10262413 chr2:10260482-10260491 chr2:10262402-10262411 chr2:10260438-10260447 chr2:10260482-10260496 chr2:10260487-10260496 chr2:10260482-10260491 chr2:10260477-10260491 chr2:10260481-10260491 chr2:10262401-10262413 chr2:10260480-10260492 chr2:10260487-10260496 chr2:10260481-10260491 chr2:10260485-10260497 chr2:10263302-10263311 chr2:10260437-10260449 chr2:10260437-10260449 chr2:10263304-10263317 chr2:10260480-10260492 chr2:10260579-10260590 chr2:10260439-10260448 chr2:10260486-10260495
2	POLR2A	chr2:10259419-10264186	PANC-1	pancreas:	n/a	n/a
3	SP4	chr2:10262647-10263428	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr2:10262639-10263248	GM12891	blood:	n/a	n/a
5	MXI1	chr2:10262580-10263346	K562	blood:	n/a	n/a
6	ZMIZ1	chr2:10261337-10263174	K562	blood:	n/a	n/a
7	MAX	chr2:10261490-10263449	K562	blood:	n/a	chr2:10263195-10263204 chr2:10262177-10262186
8	TAF1	chr2:10261715-10263405	K562	blood:	n/a	n/a
9	HMGN3	chr2:10262109-10263466	K562	blood:	n/a	n/a
10	E2F4	chr2:10262449-10263149	GM12878	blood:	n/a	chr2:10262825-10262836
11	SMARCB1	chr2:10261831-10263794	Hela-S3	cervix:	n/a	n/a
12	TAF1	chr2:10262675-10263084	SK-N-SH	brain:	n/a	n/a
13	ZBTB7A	chr2:10262098-10262927	HepG2	liver:	n/a	chr2:10262221-10262232
14	ZBTB7A	chr2:10261893-10263599	ECC-1	luminal epithelium:	n/a	chr2:10262221-10262232
15	ETS1	chr2:10262208-10263432	K562	blood:	n/a	chr2:10262611-10262620 chr2:10262696-10262705 chr2:10262302-10262313
16	ZBTB33	chr2:10261857-10263078	A549	lung:	n/a	chr2:10262541-10262551 chr2:10262544-10262554
17	POLR2A	chr2:10261832-10263353	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F6	chr2:10261521-10263571	H1-hESC	embryonic stem cell:	n/a	chr2:10263286-10263298 chr2:10263232-10263243 chr2:10263232-10263243 chr2:10262368-10262378 chr2:10262230-10262238 chr2:10263232-10263243 chr2:10263232-10263243 chr2:10263236-10263243 chr2:10263229-10263246 chr2:10263287-10263294 chr2:10262228-10262239 chr2:10262825-10262836 chr2:10262402-10262411 chr2:10262229-10262239 chr2:10263287-10263294 chr2:10262231-10262238 chr2:10263233-10263248 chr2:10263227-10263242 chr2:10263287-10263294 chr2:10262230-10262238 chr2:10263232-10263243 chr2:10263235-10263243
19	YY1	chr2:10262058-10263251	HepG2	liver:	n/a	chr2:10262405-10262419 chr2:10262567-10262581 chr2:10262664-10262678 chr2:10262567-10262576 chr2:10262707-10262721 chr2:10262658-10262672 chr2:10262709-10262718 chr2:10262570-10262579 chr2:10262370-10262379
20	TCF12	chr2:10262179-10263362	ECC-1	luminal epithelium:	n/a	n/a
21	JUND	chr2:10261791-10263084	K562	blood:	n/a	chr2:10262401-10262410 chr2:10262054-10262065
22	SIN3AK20	chr2:10262168-10263509	K562	blood:	n/a	n/a
23	MAX	chr2:10261836-10263584	H1-hESC	embryonic stem cell:	n/a	chr2:10263195-10263204 chr2:10262177-10262186
24	SIN3AK20	chr2:10262703-10263047	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr2:10261972-10263302	HUVEC	blood vessel:	n/a	n/a
26	HEY1	chr2:10260091-10268046	K562	blood:	n/a	chr2:10262408-10262423 chr2:10262559-10262574 chr2:10262366-10262381 chr2:10260481-10260496 chr2:10262702-10262717 chr2:10262368-10262383 chr2:10262406-10262421 chr2:10260417-10260432
27	E2F6	chr2:10261849-10263476	K562	blood:	n/a	chr2:10263286-10263298 chr2:10263232-10263243 chr2:10263232-10263243 chr2:10262368-10262378 chr2:10262230-10262238 chr2:10263232-10263243 chr2:10263232-10263243 chr2:10263236-10263243 chr2:10263229-10263246 chr2:10263287-10263294 chr2:10262228-10262239 chr2:10262825-10262836 chr2:10262402-10262411 chr2:10262229-10262239 chr2:10263287-10263294 chr2:10262231-10262238 chr2:10263233-10263248 chr2:10263227-10263242 chr2:10263287-10263294 chr2:10262230-10262238 chr2:10263232-10263243 chr2:10263235-10263243
28	IRF1	chr2:10260158-10263117	K562	blood:	n/a	chr2:10260480-10260494 chr2:10260485-10260499 chr2:10262401-10262415 chr2:10260437-10260451 chr2:10261543-10261552 chr2:10261541-10261551 chr2:10261082-10261099
29	BCLAF1	chr2:10262423-10263207	K562	blood:	n/a	chr2:10262709-10262722 chr2:10262568-10262577
30	SIN3AK20	chr2:10262694-10263421	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:10262662-10263123	U87	brain:	n/a	n/a
32	HA-E2F1	chr2:10262150-10263479	Hela-S3	cervix:	n/a	chr2:10263286-10263298 chr2:10263232-10263243 chr2:10262824-10262835 chr2:10263232-10263243 chr2:10262368-10262378 chr2:10262230-10262238 chr2:10263232-10263243 chr2:10263232-10263243 chr2:10263236-10263243 chr2:10263229-10263246 chr2:10263287-10263294 chr2:10262228-10262239 chr2:10262402-10262411 chr2:10262229-10262239 chr2:10263287-10263294 chr2:10262231-10262238 chr2:10263233-10263248 chr2:10263227-10263242 chr2:10263287-10263294 chr2:10262230-10262238 chr2:10263232-10263243
33	CTCF	chr2:10262800-10262950	WERI-Rb-1	eye:	n/a	n/a
34	FOXP2	chr2:10262590-10263354	PFSK-1	brain:	n/a	n/a
35	BRCA1	chr2:10262199-10263004	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr2:10261801-10263530	H1-hESC	embryonic stem cell:	n/a	n/a
37	ZNF263	chr2:10260269-10263460	HEK293-T-REx	kidney:	n/a	chr2:10262384-10262393
38	PAX5	chr2:10262569-10263191	GM12878	blood:	n/a	n/a
39	CTCF	chr2:10262918-10262942	NHEK	skin:	n/a	n/a
40	JUN	chr2:10259967-10263542	K562	blood:	n/a	chr2:10262401-10262410 chr2:10260480-10260489 chr2:10260855-10260865 chr2:10260856-10260864 chr2:10260485-10260494 chr2:10260856-10260864 chr2:10260856-10260863
41	FOXM1	chr2:10261990-10263482	ECC-1	luminal epithelium:	n/a	n/a
42	ELF1	chr2:10262297-10263042	GM12878	blood:	n/a	chr2:10262567-10262576 chr2:10262367-10262376
43	SP1	chr2:10262661-10262997	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr2:10261814-10263454	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:10260183-10263119	MCF10A-Er-Src	breast:	n/a	n/a
46	MAX	chr2:10261789-10263540	ECC-1	luminal epithelium:	n/a	chr2:10263195-10263204 chr2:10262177-10262186
47	POLR2A	chr2:10262203-10263239	A549	lung:	n/a	n/a
48	POLR2A	chr2:10262067-10263094	HepG2	liver:	n/a	n/a
49	MXI1	chr2:10261646-10264915	IMR90	lung:	n/a	n/a
50	PML	chr2:10262573-10263148	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:120924187..120925128-chr2:10262423..10262961,2	HCT-116	colon:
2	chr2:9983262..9985223-chr2:10260728..10263822,3	K562	blood:
3	chr2:10262383..10263291-chr5:43514629..43515371,2	Hela-S3	cervix:
4	chr16:27560922..27561588-chr2:10262620..10263377,2	Hela-S3	cervix:
5	chr2:10262306..10264072-chr2:10830698..10832625,2	K562	blood:
6	chr2:10259653..10265917-chr2:10585320..10590295,8	MCF-7	breast:
7	chr1:149858442..149858973-chr2:10262178..10262943,2	Hela-S3	cervix:
8	chr2:10262864..10263458-chr5:36876574..36877166,2	NB4	blood:
9	chr2:10262427..10262927-chr22:36924793..36925294,2	HCT-116	colon:
10	chr2:10259839..10264771-chr2:10582056..10590038,19	K562	blood:
11	chr15:65596954..65598103-chr2:10262171..10263178,3	Hela-S3	cervix:
12	chr2:10261562..10263628-chr2:10332391..10333942,2	K562	blood:
13	chr2:10217388..10221351-chr2:10260365..10264430,6	K562	blood:
14	chr1:154947408..154948016-chr2:10262107..10263095,2	Hela-S3	cervix:
15	chr2:10181815..10186886-chr2:10257895..10263826,12	K562	blood:
16	chr2:10181485..10190041-chr2:10258160..10265104,19	K562	blood:
17	chr2:10257984..10265070-chr2:10582045..10589780,17	K562	blood:
18	chr2:10261047..10264754-chr2:10441936..10445688,4	MCF-7	breast:
19	chr2:9769329..9772234-chr2:10259369..10263419,6	K562	blood:
20	chr2:10182809..10185071-chr2:10261991..10263522,2	MCF-7	breast:
21	chr2:10262824..10265094-chr2:10557551..10560523,2	K562	blood:
22	chr2:10262414..10263095-chrX:23760984..23761755,2	Hela-S3	cervix:
23	chr19:2782943..2783480-chr2:10262747..10263298,2	Hela-S3	cervix:
24	chr2:10262275..10263092-chr5:114598074..114598869,2	HCT-116	colon:
25	chr2:10262501..10263375-chr7:66119471..66120046,2	Hela-S3	cervix:
26	chr2:10222068..10224764-chr2:10261306..10263979,2	K562	blood:
27	chr2:10259710..10265084-chr2:10586364..10590442,7	MCF-7	breast:
28	chr2:10260909..10263628-chr2:10332391..10334618,3	K562	blood:
29	chr2:10262407..10262923-chr9:130213627..130214191,2	Hela-S3	cervix:
30	chr12:46765626..46766493-chr2:10262224..10262953,2	Hela-S3	cervix:
31	chr2:10262448..10263200-chr3:122785730..122786424,2	Hela-S3	cervix:
32	chr2:10262865..10263445-chr22:32149498..32150087,2	Hela-S3	cervix:
33	chr2:10229570..10233123-chr2:10259464..10263291,4	K562	blood:
34	chr2:10260822..10263290-chr5:172330317..172332329,2	MCF-7	breast:
35	chr2:10262416..10262948-chr6:35656174..35657022,2	NB4	blood:

Variant related genes	Relation type
RRM2	TF binding region
ENSG00000172244	Chromatin interaction
ENSG00000265418	Chromatin interaction
ENSG00000243819	Chromatin interaction
ENSG00000065485	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000271797	Chromatin interaction
ENSG00000172059	Chromatin interaction
ENSG00000257135	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000096060	Chromatin interaction
ENSG00000104969	Chromatin interaction
ENSG00000047578	Chromatin interaction
ENSG00000113719	Chromatin interaction
ENSG00000115756	Chromatin interaction
ENSG00000183605	Chromatin interaction
ENSG00000077235	Chromatin interaction
ENSG00000134308	Chromatin interaction
ENSG00000115750	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000148356	Chromatin interaction
ENSG00000100353	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000212558	Chromatin interaction
ENSG00000164190	Chromatin interaction
ENSG00000233502	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000123130	Chromatin interaction
ENSG00000205795	Chromatin interaction
ENSG00000164219	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10197121	0.81[JPT][hapmap]
rs11896140	0.81[JPT][hapmap]
rs13392622	0.95[ASN][1000 genomes]
rs2110641	0.81[JPT][hapmap]
rs2110643	0.97[ASN][1000 genomes]
rs2160190	0.84[CEU][hapmap]
rs2241113	0.81[JPT][hapmap]
rs34455011	0.86[ASN][1000 genomes]
rs4309551	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4668664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6432062	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6432064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6432065	0.98[ASN][1000 genomes]
rs6432066	0.82[CEU][hapmap]
rs6432068	0.81[JPT][hapmap]
rs6706570	0.81[JPT][hapmap]
rs6715884	0.97[ASN][1000 genomes]
rs6737932	0.98[ASN][1000 genomes]
rs6741290	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6749325	0.81[JPT][hapmap]
rs6759180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs717886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs718215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs729917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7577887	0.98[ASN][1000 genomes]
rs7603436	0.96[ASN][1000 genomes]
rs7604817	0.93[ASN][1000 genomes]
rs7605457	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv873633	chr2:10175442-10266563	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
7	nsv1010706	chr2:10189219-10266995	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10260000-10263400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:10260000-10263600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:10260000-10263800	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:10260000-10264200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:10260200-10263200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr2:10260200-10263600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr2:10260200-10263600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:10260200-10263600	Active TSS	A549	lung
9	chr2:10260200-10263600	Active TSS	K562	blood
10	chr2:10260200-10263800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:10260200-10263800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr2:10260200-10264200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:10260200-10264200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:10260200-10264400	Active TSS	H1 Cell Line	embryonic stem cell
15	chr2:10260200-10264400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr2:10260200-10264400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr2:10260200-10265000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:10260400-10264600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:10260600-10263800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr2:10260600-10265200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:10260800-10264800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr2:10261000-10263200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr2:10261000-10263600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr2:10261200-10263000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:10261200-10263000	Enhancers	Fetal Brain Male	brain
26	chr2:10261400-10263600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:10261400-10263600	Active TSS	Fetal Kidney	kidney
28	chr2:10261400-10263600	Active TSS	HSMM	muscle
29	chr2:10261600-10263400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:10261800-10263800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:10261800-10264200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:10261800-10264200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr2:10261800-10264800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr2:10262000-10263200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:10262000-10263400	Active TSS	Small Intestine	intestine
36	chr2:10262000-10263600	Active TSS	NHDF-Ad	bronchial
37	chr2:10262000-10263800	Active TSS	Hela-S3	cervix
38	chr2:10262000-10264200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:10262000-10264200	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr2:10262000-10265000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:10262200-10263000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:10262200-10263000	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr2:10262200-10263400	Transcr. at gene 5' and 3'	Right Atrium	heart
44	chr2:10262200-10263400	Flanking Active TSS	Right Ventricle	heart
45	chr2:10262200-10263400	Active TSS	Thymus	Thymus
46	chr2:10262200-10263600	Active TSS	GM12878-XiMat	blood
47	chr2:10262200-10263800	Active TSS	HSMMtube	muscle
48	chr2:10262400-10263000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:10262400-10263000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:10262400-10263000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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