Variant report

Variant	rs12488480
Chromosome Location	chr3:156885143-156885144
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	GATA3	chr3:156884975-156885818	MCF-7	breast:	n/a	chr3:156885147-156885168
2	GATA3	chr3:156884837-156885700	MCF-7	breast:	n/a	chr3:156885147-156885168
3	GATA3	chr3:156885090-156885756	T-47D	breast:	n/a	chr3:156885147-156885168
4	NR2F2	chr3:156884924-156885805	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156529223..156530794-chr3:156884048..156887029,2	MCF-7	breast:
2	chr3:156532344..156534533-chr3:156884722..156886636,3	MCF-7	breast:

Variant related genes	Relation type
KRT18P34	TF binding region

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10513508	0.90[CEU][hapmap]
rs10936061	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936062	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936064	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936065	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936067	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936068	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936069	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936074	0.93[EUR][1000 genomes]
rs10936075	0.82[EUR][1000 genomes]
rs10936078	0.89[CEU][hapmap]
rs10936080	0.90[CEU][hapmap]
rs10936081	0.90[CEU][hapmap]
rs1157738	0.86[CEU][hapmap]
rs12489453	0.94[EUR][1000 genomes]
rs12489799	0.96[EUR][1000 genomes]
rs12490836	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12492801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496051	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12496111	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12497891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630209	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632562	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs12633429	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12634818	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12635088	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636125	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403104	0.86[CEU][hapmap]
rs1403106	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap]
rs1403108	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs1500924	0.90[CEU][hapmap];0.92[JPT][hapmap]
rs1522392	0.90[CEU][hapmap]
rs1568611	0.90[CEU][hapmap];0.84[CHB][hapmap]
rs16827308	0.87[CEU][hapmap]
rs16827318	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16827322	0.86[CEU][hapmap]
rs16827352	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17552941	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995304	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2047648	0.85[CEU][hapmap]
rs2321740	0.88[EUR][1000 genomes]
rs2874616	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap]
rs35910014	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3935750	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272613	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4371471	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383467	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413278	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4608646	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes]
rs4680340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680347	0.86[CEU][hapmap]
rs4680349	0.85[EUR][1000 genomes]
rs4680352	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs4680354	0.90[CEU][hapmap]
rs5003893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828309	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835412	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55949516	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55953639	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56078410	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56263456	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57322659	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57511361	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59210914	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59279023	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59485606	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59865540	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60153077	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61149035	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62274129	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62274155	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274156	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274159	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276460	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276465	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276470	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276471	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276474	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276475	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276479	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276480	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276488	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62276489	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276490	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276491	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276495	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276496	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276497	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276501	0.96[EUR][1000 genomes]
rs62276502	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276504	0.94[EUR][1000 genomes]
rs62276505	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441119	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767619	0.81[CEU][hapmap]
rs6768052	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6768074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.93[EUR][1000 genomes]
rs6780205	0.93[EUR][1000 genomes]
rs6781682	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788214	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs6792479	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6799567	0.90[CEU][hapmap];0.92[JPT][hapmap]
rs6805989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806232	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73154633	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73154649	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154657	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73154659	0.94[EUR][1000 genomes]
rs73154671	0.86[EUR][1000 genomes]
rs73154682	0.84[EUR][1000 genomes]
rs73873800	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7610214	0.82[EUR][1000 genomes]
rs7621912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626589	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7631257	0.90[CEU][hapmap]
rs7633004	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649737	0.90[CEU][hapmap];0.84[CHB][hapmap]
rs7652298	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs8180056	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180057	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949854	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156879000-156885600	Weak transcription	Psoas Muscle	Psoas
2	chr3:156879000-156891800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:156879000-156892000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:156879200-156891800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:156879200-156891800	Weak transcription	Fetal Stomach	stomach
6	chr3:156879200-156891800	Weak transcription	Fetal Thymus	thymus
7	chr3:156879200-156892000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:156879400-156891200	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:156879800-156891800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:156880000-156888800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:156880000-156891400	Weak transcription	Placenta	Placenta
12	chr3:156880000-156891400	Weak transcription	GM12878-XiMat	blood
13	chr3:156880200-156888400	Weak transcription	Primary B cells from cord blood	blood
14	chr3:156880200-156891600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:156880200-156891800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:156880400-156891600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:156881000-156891600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:156881200-156892200	Weak transcription	Small Intestine	intestine
19	chr3:156881800-156888400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:156881800-156892000	Weak transcription	Lung	lung
21	chr3:156883000-156885800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:156883600-156886200	Enhancers	Liver	Liver
23	chr3:156883800-156886200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr3:156884000-156886000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:156884000-156886600	Enhancers	Fetal Intestine Small	intestine
26	chr3:156884000-156886800	Enhancers	Fetal Intestine Large	intestine
27	chr3:156884200-156885600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr3:156884400-156885200	Enhancers	Fetal Kidney	kidney
29	chr3:156885000-156885400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:156885000-156885600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:156885000-156886000	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:156885000-156891800	Weak transcription	HepG2	liver

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