Variant report

Variant	rs6746757
Chromosome Location	chr2:55538522-55538523
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	EBF1	chr2:55538405-55539303	GM12878	blood:	n/a	n/a
2	POU2F2	chr2:55538516-55539051	GM12878	blood:	n/a	n/a
3	IKZF1	chr2:55538450-55538823	GM12878	blood:	n/a	n/a
4	PBX3	chr2:55538509-55539086	SK-N-SH	brain:	n/a	n/a
5	RUNX3	chr2:55538401-55539070	GM12878	blood:	n/a	n/a
6	BATF	chr2:55538455-55539013	GM12878	blood:	n/a	n/a
7	EP300	chr2:55538502-55538966	SK-N-SH_RA	brain:	n/a	n/a
8	PML	chr2:55538314-55539187	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:55538195-55539113	GM12878	blood:	n/a	n/a
10	MEF2C	chr2:55538469-55539111	GM12878	blood:	n/a	chr2:55538774-55538789
11	BCL3	chr2:55538496-55539033	GM12878	blood:	n/a	n/a
12	IRF4	chr2:55538474-55539072	GM12878	blood:	n/a	n/a
13	BHLHE40	chr2:55538500-55539062	GM12878	blood:	n/a	n/a
14	STAT5A	chr2:55538471-55539070	GM12878	blood:	n/a	chr2:55538841-55538850 chr2:55538842-55538851
15	MTA3	chr2:55538368-55539069	GM12878	blood:	n/a	n/a
16	CREB1	chr2:55538359-55539061	GM12878	blood:	n/a	n/a
17	TCF12	chr2:55538406-55539140	SK-N-SH	brain:	n/a	n/a
18	FOSL2	chr2:55538511-55539081	SK-N-SH	brain:	n/a	n/a
19	MTA3	chr2:55538330-55539096	GM12878	blood:	n/a	n/a
20	FOXM1	chr2:55538357-55539171	GM12878	blood:	n/a	n/a
21	MEF2A	chr2:55538384-55538976	GM12878	blood:	n/a	n/a
22	BCL11A	chr2:55538417-55539027	GM12878	blood:	n/a	n/a
23	BCL11A	chr2:55538483-55539067	GM12878	blood:	n/a	n/a
24	EP300	chr2:55538496-55539040	SK-N-SH_RA	brain:	n/a	n/a
25	NFATC1	chr2:55538378-55539035	GM12878	blood:	n/a	n/a
26	ATF2	chr2:55538284-55539073	GM12878	blood:	n/a	n/a
27	BCLAF1	chr2:55538437-55539096	GM12878	blood:	n/a	n/a
28	POU2F2	chr2:55538481-55538909	GM12891	blood:	n/a	n/a
29	BATF	chr2:55538437-55539121	GM12878	blood:	n/a	n/a
30	EP300	chr2:55538501-55539019	GM12878	blood:	n/a	n/a
31	JUND	chr2:55538093-55539228	SK-N-SH	brain:	n/a	chr2:55538203-55538213 chr2:55538840-55538851
32	TCF3	chr2:55538522-55538976	GM12878	blood:	n/a	n/a
33	FOXM1	chr2:55538300-55539072	GM12878	blood:	n/a	n/a
34	ATF2	chr2:55538318-55539135	GM12878	blood:	n/a	n/a
35	CEBPB	chr2:55538323-55539139	GM12878	blood:	n/a	n/a
36	NFIC	chr2:55538362-55539059	GM12878	blood:	n/a	n/a
37	BCLAF1	chr2:55538467-55539105	GM12878	blood:	n/a	n/a
38	NFIC	chr2:55538195-55539136	GM12878	blood:	n/a	n/a
39	NFATC1	chr2:55538310-55539095	GM12878	blood:	n/a	n/a
40	MEF2A	chr2:55538347-55539071	GM12878	blood:	n/a	n/a
41	CTCF	chr2:55538480-55538630	AG10803	skin:	n/a	n/a
42	STAT5A	chr2:55538411-55539044	GM12878	blood:	n/a	chr2:55538841-55538850 chr2:55538842-55538851

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55536648..55539597-chr2:55541310..55544144,3	K562	blood:

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000240401	TF binding region
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10153861	0.98[AFR][1000 genomes]
rs10181997	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs10183953	1.00[CEU][hapmap]
rs10184362	0.95[AFR][1000 genomes]
rs10186158	0.90[AFR][1000 genomes]
rs10191785	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10194658	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10196295	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10199332	0.84[AFR][1000 genomes]
rs10201075	0.97[AFR][1000 genomes]
rs10202943	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10209908	0.95[AFR][1000 genomes]
rs10439479	1.00[CEU][hapmap]
rs10518764	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs11694920	1.00[CEU][hapmap]
rs12464094	1.00[CEU][hapmap]
rs13384739	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs13389151	0.80[AFR][1000 genomes]
rs13389799	0.95[AFR][1000 genomes]
rs13390100	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs13398447	0.93[AFR][1000 genomes]
rs13402277	0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs13404740	0.98[AFR][1000 genomes]
rs13406929	0.93[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs13408706	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs13412682	0.95[YRI][hapmap];0.97[AFR][1000 genomes]
rs13416519	0.98[AFR][1000 genomes]
rs13423955	0.82[YRI][hapmap]
rs13426160	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs13426766	0.91[YRI][hapmap]
rs13429863	0.80[AFR][1000 genomes]
rs1437389	1.00[CEU][hapmap]
rs1437392	1.00[CEU][hapmap]
rs1545554	0.82[LWK][hapmap]
rs1561231	1.00[CEU][hapmap]
rs17046828	1.00[ASW][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes]
rs17046837	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17046881	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs17046896	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs17046915	1.00[CEU][hapmap]
rs17046954	0.80[AFR][1000 genomes]
rs17264948	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs1902057	0.82[LWK][hapmap]
rs2043714	1.00[CEU][hapmap]
rs2043716	0.80[AFR][1000 genomes]
rs2118283	1.00[CEU][hapmap]
rs2123983	0.82[LWK][hapmap]
rs2164715	1.00[CEU][hapmap]
rs28434193	0.91[AFR][1000 genomes]
rs3099080	0.84[LWK][hapmap]
rs3861571	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs3975804	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs4233959	1.00[CEU][hapmap]
rs4591380	1.00[CEU][hapmap]
rs6545476	1.00[CEU][hapmap]
rs6545479	1.00[CEU][hapmap]
rs6545485	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes]
rs6545486	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes]
rs6704701	0.98[AFR][1000 genomes]
rs6707774	0.93[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes]
rs6713058	1.00[CEU][hapmap]
rs6715694	1.00[CEU][hapmap]
rs6715991	0.98[AFR][1000 genomes]
rs6716066	1.00[CEU][hapmap]
rs6717221	0.81[AFR][1000 genomes]
rs6719579	1.00[CEU][hapmap]
rs6723870	1.00[CEU][hapmap]
rs6729144	1.00[ASW][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6738517	0.85[YRI][hapmap]
rs6746983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6747682	1.00[CEU][hapmap]
rs6747974	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6748541	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6750501	1.00[CEU][hapmap]
rs6758229	0.97[AFR][1000 genomes]
rs6759310	1.00[CEU][hapmap]
rs6759625	1.00[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6759763	0.96[YRI][hapmap];0.98[AFR][1000 genomes]
rs6759957	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6761771	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs72918961	0.93[AFR][1000 genomes]
rs72918964	0.95[AFR][1000 genomes]
rs72918965	0.95[AFR][1000 genomes]
rs72918972	0.95[AFR][1000 genomes]
rs72923156	0.98[AFR][1000 genomes]
rs72923157	0.98[AFR][1000 genomes]
rs72923187	0.80[AFR][1000 genomes]
rs72927374	0.95[EUR][1000 genomes]
rs7561604	0.80[AFR][1000 genomes]
rs7577510	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs7594907	0.91[AFR][1000 genomes]
rs7606361	0.82[LWK][hapmap]
rs9309264	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
4	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
7	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
8	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
11	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
15	chr2:55512600-55546000	Weak transcription	Small Intestine	intestine
16	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
20	chr2:55520000-55538800	Weak transcription	Ovary	ovary
21	chr2:55520000-55541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:55520200-55539000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:55523000-55538800	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:55523000-55548000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
29	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:55523600-55541000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:55523600-55542000	Weak transcription	Fetal Brain Male	brain
32	chr2:55523600-55548000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:55523800-55541000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:55524000-55541200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:55524400-55538800	Weak transcription	Left Ventricle	heart
37	chr2:55524800-55543200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:55524800-55549400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:55526400-55549600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:55527000-55546400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:55527400-55539600	Weak transcription	K562	blood
42	chr2:55527400-55541000	Weak transcription	Brain Anterior Caudate	brain
43	chr2:55527600-55540000	Weak transcription	Fetal Kidney	kidney
44	chr2:55528600-55542000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:55529400-55544400	Weak transcription	Placenta	Placenta
46	chr2:55532200-55543800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:55533000-55542000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:55533000-55544000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:55534200-55538600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:55534200-55538600	Weak transcription	Brain Hippocampus Middle	brain

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