Variant report

Variant	rs12360577
Chromosome Location	chr11:28130475-28130476
allele	A/C
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	FOS	chr11:28130403-28130844	HUVEC	blood vessel:	n/a	chr11:28130652-28130661 chr11:28130651-28130663 chr11:28130652-28130662 chr11:28130653-28130662 chr11:28130651-28130662 chr11:28130653-28130660 chr11:28130653-28130661
2	EP300	chr11:28129437-28130574	K562	blood:	n/a	chr11:28129458-28129472
3	POLR2A	chr11:28128303-28130602	K562	blood:	n/a	n/a
4	IRF1	chr11:28128785-28132204	K562	blood:	n/a	chr11:28130092-28130106 chr11:28132180-28132190 chr11:28129456-28129467 chr11:28132179-28132190 chr11:28129742-28129751 chr11:28129457-28129471 chr11:28130652-28130661 chr11:28132179-28132192 chr11:28129451-28129468 chr11:28132180-28132194 chr11:28132159-28132169 chr11:28129453-28129467 chr11:28130653-28130662 chr11:28130276-28130292 chr11:28129457-28129467 chr11:28129898-28129912
5	JUND	chr11:28129416-28130863	K562	blood:	n/a	chr11:28130652-28130661 chr11:28130651-28130663 chr11:28130652-28130662 chr11:28130651-28130662 chr11:28129760-28129769 chr11:28130653-28130662 chr11:28130653-28130660 chr11:28130653-28130661
6	HCFC1	chr11:28128551-28132891	Hela-S3	cervix:	n/a	n/a
7	JUND	chr11:28130448-28130835	Hela-S3	cervix:	n/a	chr11:28130652-28130661 chr11:28130651-28130663 chr11:28130652-28130662 chr11:28130651-28130662 chr11:28130653-28130662 chr11:28130653-28130660 chr11:28130653-28130661
8	CHD1	chr11:28127516-28133124	IMR90	lung:	n/a	n/a
9	E2F4	chr11:28128634-28130842	MCF10A-Er-Src	breast:	n/a	chr11:28129742-28129751 chr11:28129799-28129807 chr11:28129707-28129716 chr11:28129800-28129811 chr11:28129800-28129811 chr11:28129795-28129810
10	MXI1	chr11:28128494-28130513	SK-N-SH	brain:	n/a	chr11:28129853-28129868 chr11:28129851-28129866
11	FOS	chr11:28130474-28130899	MCF10A-Er-Src	breast:	n/a	chr11:28130652-28130661 chr11:28130651-28130663 chr11:28130652-28130662 chr11:28130653-28130662 chr11:28130651-28130662 chr11:28130653-28130660 chr11:28130653-28130661
12	POLR2A	chr11:28128618-28133315	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr11:28128768-28130893	MCF10A-Er-Src	breast:	n/a	n/a
14	JUND	chr11:28130452-28130833	HepG2	liver:	n/a	chr11:28130652-28130661 chr11:28130651-28130663 chr11:28130652-28130662 chr11:28130651-28130662 chr11:28130653-28130662 chr11:28130653-28130660 chr11:28130653-28130661
15	FOS	chr11:28130474-28130832	MCF10A-Er-Src	breast:	n/a	chr11:28130652-28130661 chr11:28130651-28130663 chr11:28130652-28130662 chr11:28130653-28130662 chr11:28130651-28130662 chr11:28130653-28130660 chr11:28130653-28130661
16	POLR2A	chr11:28127056-28133217	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:27720668..27722318-chr11:28128982..28131209,2	K562	blood:
2	chr11:28109457..28114011-chr11:28125325..28130505,4	K562	blood:

Variant related genes	Relation type
KIF18A	TF binding region
METTL15	TF binding region
ENSG00000176697	Chromatin interaction
ENSG00000121621	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1032090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1032091	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10767697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10767705	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10767710	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835259	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835275	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10835282	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835286	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835294	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10835296	0.96[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10835298	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835310	0.82[ASN][1000 genomes]
rs11030193	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11030197	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11030201	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11030203	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11030204	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11030223	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11030227	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11030228	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11030259	0.81[EUR][1000 genomes]
rs11030262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11030267	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12294035	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12361167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12806548	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1384904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1483861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1564745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1608871	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17244296	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2046372	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2128956	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2128958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2140886	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140887	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2354426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4923522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923525	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6484352	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6484357	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6484361	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6484366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7105075	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7107992	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7108140	0.93[EUR][1000 genomes]
rs7121923	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7127104	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7128488	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7129953	0.87[EUR][1000 genomes]
rs7482650	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7924896	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7932126	0.82[ASN][1000 genomes]
rs7944852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs960357	0.96[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs997555	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9988877	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832096	chr11:28020435-28155586	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv553915	chr11:28071479-28138709	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv897150	chr11:28110210-28302792	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1040043	chr11:28118451-28170684	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv897151	chr11:28130191-28208464	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv897152	chr11:28130191-28218303	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr11:28126800-28130800	Active TSS	NHLF	lung
2	chr11:28126800-28133400	Active TSS	K562	blood
3	chr11:28127200-28133000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:28127800-28130600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:28127800-28133400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr11:28128000-28130600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:28128000-28130600	Active TSS	NHDF-Ad	bronchial
8	chr11:28128000-28130600	Active TSS	NHEK	skin
9	chr11:28128000-28133000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr11:28128200-28130800	Active TSS	HMEC	breast
11	chr11:28128200-28131200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:28128200-28131400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:28128400-28130600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr11:28128400-28130600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:28128400-28132400	Active TSS	Brain Germinal Matrix	brain
16	chr11:28128600-28130600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:28128600-28130600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:28128600-28130600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr11:28128600-28130600	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr11:28128600-28130800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:28128600-28130800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:28128800-28130600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr11:28128800-28130600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr11:28128800-28130600	Active TSS	Fetal Intestine Large	intestine
25	chr11:28128800-28130600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr11:28128800-28130600	Active TSS	HSMMtube	muscle
27	chr11:28128800-28131200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:28129000-28130800	Active TSS	Fetal Kidney	kidney
29	chr11:28129400-28130600	Active TSS	Brain Angular Gyrus	brain
30	chr11:28129400-28130600	Active TSS	Fetal Stomach	stomach
31	chr11:28129400-28130600	Active TSS	Stomach Smooth Muscle	stomach
32	chr11:28129400-28132400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr11:28129400-28132600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:28129600-28130600	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr11:28129600-28130800	Active TSS	Fetal Muscle Leg	muscle
36	chr11:28129800-28131800	Weak transcription	Small Intestine	intestine
37	chr11:28130000-28130600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr11:28130000-28130600	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr11:28130000-28130600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr11:28130000-28130800	Flanking Active TSS	NH-A	brain
41	chr11:28130000-28131000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr11:28130000-28131600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:28130000-28131800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr11:28130000-28131800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:28130200-28130600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr11:28130200-28130600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:28130200-28130600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr11:28130200-28130600	Flanking Active TSS	Fetal Brain Female	brain
49	chr11:28130200-28130600	Active TSS	HepG2	liver
50	chr11:28130200-28130600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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