Variant report

Variant	rs12513951
Chromosome Location	chr5:75840225-75840226
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	RAD21	chr5:75840111-75840586	ECC-1	luminal epithelium:	n/a	chr5:75840321-75840340
2	RAD21	chr5:75840112-75840437	GM12878	blood:	n/a	chr5:75840321-75840340
3	HCFC1	chr5:75840222-75840417	K562	blood:	n/a	n/a
4	CTCF	chr5:75840074-75840512	H1-hESC	embryonic stem cell:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
5	EBF1	chr5:75839964-75840457	GM12878	blood:	n/a	chr5:75840109-75840120
6	ZNF143	chr5:75840210-75840477	K562	blood:	n/a	n/a
7	CTCF	chr5:75840154-75840431	SK-N-SH_RA	brain:	n/a	chr5:75840318-75840339
8	CTCF	chr5:75840213-75840464	MCF-7	breast:	n/a	chr5:75840318-75840339
9	CTCF	chr5:75840222-75840462	MCF-7	breast:	n/a	chr5:75840318-75840339
10	POLR2A	chr5:75838483-75840557	PBDE	blood:	n/a	n/a
11	CTCF	chr5:75840224-75840446	Fibrobl	skin:	n/a	chr5:75840318-75840339
12	CTCF	chr5:75840180-75840330	BJ	skin:	n/a	n/a
13	ZNF143	chr5:75840153-75840514	GM12878	blood:	n/a	n/a
14	CTCF	chr5:75840134-75840467	HepG2	liver:	n/a	chr5:75840318-75840339
15	CTCF	chr5:75840213-75840459	A549	lung:	n/a	chr5:75840318-75840339
16	CTCF	chr5:75840205-75840479	Pancreas_OC	pancreas:	n/a	chr5:75840318-75840339
17	CTCF	chr5:75840112-75840440	T-47D	breast:	n/a	chr5:75840318-75840339
18	ARID3A	chr5:75840098-75840519	HepG2	liver:	n/a	n/a
19	ATF2	chr5:75840097-75840472	H1-hESC	embryonic stem cell:	n/a	n/a
20	RCOR1	chr5:75840207-75840438	HepG2	liver:	n/a	n/a
21	CTCF	chr5:75840178-75840492	IMR90	lung:	n/a	chr5:75840318-75840339
22	CTCF	chr5:75840200-75840350	GM12864	blood:	n/a	chr5:75840318-75840339
23	RAD21	chr5:75840069-75840449	HepG2	liver:	n/a	chr5:75840321-75840340
24	CTCF	chr5:75840200-75840350	GM12866	blood:	n/a	chr5:75840318-75840339
25	SMC3	chr5:75840124-75840515	K562	blood:	n/a	chr5:75840325-75840339
26	CTCF	chr5:75840205-75840433	HepG2	liver:	n/a	chr5:75840318-75840339
27	JUND	chr5:75840157-75840480	K562	blood:	n/a	n/a
28	RAD21	chr5:75840077-75840569	A549	lung:	n/a	chr5:75840321-75840340
29	CTCF	chr5:75840220-75840370	GM12874	blood:	n/a	chr5:75840318-75840339
30	CTCF	chr5:75840108-75840531	T-47D	breast:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
31	RAD21	chr5:75840128-75840600	MCF-7	breast:	n/a	chr5:75840321-75840340
32	CTCF	chr5:75840200-75840350	GM12801	blood:	n/a	chr5:75840318-75840339
33	SMC3	chr5:75840113-75840534	HepG2	liver:	n/a	chr5:75840325-75840339
34	CTCF	chr5:75840206-75840434	A549	lung:	n/a	chr5:75840318-75840339
35	RAD21	chr5:75840149-75840474	ECC-1	luminal epithelium:	n/a	chr5:75840321-75840340
36	WRNIP1	chr5:75839886-75840432	GM12878	blood:	n/a	n/a
37	CTCF	chr5:75840194-75840480	MCF-7	breast:	n/a	chr5:75840318-75840339
38	RFX5	chr5:75840181-75840480	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr5:75840220-75840370	NHEK	skin:	n/a	chr5:75840318-75840339
40	RAD21	chr5:75840066-75840489	H1-hESC	embryonic stem cell:	n/a	chr5:75840321-75840340
41	MAZ	chr5:75839888-75840381	HepG2	liver:	n/a	chr5:75839967-75839976
42	SMC3	chr5:75839628-75840700	SK-N-SH	brain:	n/a	chr5:75840325-75840339
43	RAD21	chr5:75839999-75840617	MCF-7	breast:	n/a	chr5:75840321-75840340
44	CTCF	chr5:75840220-75840370	HEK293	kidney:	n/a	chr5:75840318-75840339
45	CTCF	chr5:75840029-75840689	HCT-116	colon:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
46	CTCF	chr5:75840204-75840464	LNCaP	prostate:	n/a	chr5:75840318-75840339
47	CTCF	chr5:75840204-75840466	LNCaP	prostate:	n/a	chr5:75840318-75840339
48	CTCF	chr5:75840216-75840489	Spleen_OC	spleen:	n/a	chr5:75840318-75840339
49	ATF1	chr5:75840185-75840485	K562	blood:	n/a	n/a
50	CTCF	chr5:75840109-75840561	MCF-7	breast:	n/a	chr5:75840111-75840120 chr5:75840318-75840339

No.	Distal block	Cell Line	Cell type
1	chr5:75698659..75699503-chr5:75839829..75840376,2	K562	blood:
2	chr5:75628819..75631136-chr5:75840007..75842103,2	K562	blood:
3	chr5:75633886..75634436-chr5:75839825..75840735,2	K562	blood:
4	chr5:75698517..75699563-chr5:75839811..75840781,6	MCF-7	breast:
5	chr5:75633417..75634381-chr5:75839891..75840630,3	MCF-7	breast:
6	chr5:75633462..75634419-chr5:75839412..75840924,7	MCF-7	breast:

Variant related genes	Relation type
IQGAP2	TF binding region
ENSG00000145703	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10044688	0.84[JPT][hapmap]
rs10064543	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065424	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10080190	0.83[JPT][hapmap]
rs10942784	0.89[JPT][hapmap]
rs13355881	0.85[CHB][hapmap]
rs2202113	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4704330	0.89[JPT][hapmap]
rs4704332	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs4704333	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6453231	0.89[JPT][hapmap]
rs6453232	0.84[JPT][hapmap]
rs6869692	0.88[JPT][hapmap]
rs6889411	0.84[JPT][hapmap]
rs7722711	0.84[JPT][hapmap]
rs7731027	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9293687	0.85[CHB][hapmap]
rs9293688	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9687487	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer 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	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75830000-75841600	Enhancers	Stomach Mucosa	stomach
2	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:75837400-75840600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr5:75837400-75842800	Enhancers	Liver	Liver
5	chr5:75837800-75840600	Enhancers	Fetal Lung	lung
6	chr5:75837800-75841200	Enhancers	Placenta	Placenta
7	chr5:75838000-75840400	Enhancers	Fetal Thymus	thymus
8	chr5:75838000-75840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:75838200-75840600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr5:75838200-75841400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:75838400-75840600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr5:75838400-75840600	Enhancers	Fetal Kidney	kidney
13	chr5:75838600-75840400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr5:75838600-75840400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:75838600-75840600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:75839000-75840400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr5:75839000-75840400	Enhancers	Lung	lung
18	chr5:75839000-75840600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:75839000-75840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:75839000-75841600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr5:75839200-75840600	Enhancers	Pancreas	Pancrea
22	chr5:75839200-75840800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr5:75839200-75841400	Enhancers	Fetal Intestine Small	intestine
24	chr5:75839400-75840400	Enhancers	Primary B cells from peripheral blood	blood
25	chr5:75839400-75840400	Enhancers	Fetal Intestine Large	intestine
26	chr5:75839400-75840600	Enhancers	Primary B cells from cord blood	blood
27	chr5:75839400-75840600	Enhancers	Primary T cells from cord blood	blood
28	chr5:75839400-75840600	Enhancers	K562	blood
29	chr5:75839400-75840600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr5:75839400-75842200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:75839400-75842400	Weak transcription	Adipose Nuclei	Adipose
32	chr5:75839400-75842600	Weak transcription	Thymus	Thymus
33	chr5:75839600-75840400	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr5:75839600-75845400	Enhancers	HepG2	liver
35	chr5:75839600-75845800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:75839600-75846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr5:75839800-75840400	Enhancers	Fetal Muscle Leg	muscle
38	chr5:75839800-75840400	Enhancers	Spleen	Spleen
39	chr5:75839800-75840600	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr5:75839800-75840600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr5:75839800-75842200	Enhancers	GM12878-XiMat	blood
42	chr5:75840000-75840600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:75840000-75841200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr5:75840000-75841600	Enhancers	Duodenum Mucosa	Duodenum
45	chr5:75840000-75842400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:75840000-75842600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr5:75840200-75840400	Enhancers	Fetal Muscle Trunk	muscle
48	chr5:75840200-75842200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:75840200-75842400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr5:75840200-75842400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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