Variant report

Variant	rs1078420
Chromosome Location	chr12:105595563-105595564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105587133..105589303-chr12:105595164..105597360,2	MCF-7	breast:
2	chr12:105592344..105594615-chr12:105595221..105597389,2	MCF-7	breast:
3	chr12:105592769..105599626-chr12:105599908..105606799,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10161339	0.95[EUR][1000 genomes]
rs1076	0.90[CEU][hapmap]
rs10861337	0.89[CEU][hapmap]
rs10861342	0.90[CEU][hapmap]
rs10861346	0.90[CEU][hapmap]
rs10861354	0.90[CEU][hapmap]
rs10861356	0.90[CEU][hapmap]
rs10861357	0.90[CEU][hapmap]
rs10861358	0.90[CEU][hapmap]
rs10861360	0.90[CEU][hapmap]
rs11112373	1.00[CEU][hapmap]
rs11112378	0.90[CEU][hapmap]
rs11112380	0.90[CEU][hapmap]
rs11112394	0.90[CEU][hapmap]
rs11112403	0.90[CEU][hapmap]
rs1196851	1.00[JPT][hapmap]
rs1196869	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1196872	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1196873	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12229846	0.89[CEU][hapmap]
rs12303948	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs12309135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316054	0.89[CEU][hapmap]
rs12318799	1.00[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs1444608	0.86[CEU][hapmap]
rs17036781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882148	1.00[CHB][hapmap]
rs2044307	0.90[CEU][hapmap]
rs2257156	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2464175	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3763991	1.00[CHB][hapmap]
rs3829297	0.90[CEU][hapmap]
rs3910855	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs57393988	0.88[ASN][1000 genomes]
rs57456392	0.88[ASN][1000 genomes]
rs60230439	0.88[ASN][1000 genomes]
rs60725801	0.88[ASN][1000 genomes]
rs61042175	0.82[ASN][1000 genomes]
rs703683	0.90[CEU][hapmap]
rs7136344	0.90[CEU][hapmap]
rs7297845	1.00[CHB][hapmap]
rs7305712	0.90[CEU][hapmap]
rs7307834	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7314155	1.00[CHB][hapmap]
rs73395723	0.82[ASN][1000 genomes]
rs73395740	0.88[ASN][1000 genomes]
rs73395770	0.88[ASN][1000 genomes]
rs73395771	0.88[ASN][1000 genomes]
rs73395772	0.88[ASN][1000 genomes]
rs73395783	0.88[ASN][1000 genomes]
rs73395785	0.88[ASN][1000 genomes]
rs73397621	0.88[ASN][1000 genomes]
rs73397624	0.88[ASN][1000 genomes]
rs935249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:105571400-105617800	Weak transcription	K562	blood
5	chr12:105576000-105595600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:105577800-105598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:105577800-105598800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr12:105577800-105599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:105577800-105602600	Strong transcription	Fetal Thymus	thymus
13	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
16	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr12:105578000-105599200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
19	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr12:105578400-105602400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:105579000-105598600	Strong transcription	HSMM	muscle
23	chr12:105579000-105605200	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr12:105579800-105596000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:105581200-105602600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:105581200-105605400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr12:105581800-105602600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:105581800-105605200	Strong transcription	Brain Germinal Matrix	brain
31	chr12:105582000-105600200	Strong transcription	Fetal Stomach	stomach
32	chr12:105582000-105602600	Strong transcription	Lung	lung
33	chr12:105582000-105603400	Strong transcription	Spleen	Spleen
34	chr12:105582600-105596000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:105582800-105598200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr12:105582800-105602600	Strong transcription	Thymus	Thymus
37	chr12:105583600-105602600	Strong transcription	Esophagus	oesophagus
38	chr12:105583600-105605600	Strong transcription	Right Ventricle	heart
39	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:105584400-105600200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:105585400-105603400	Strong transcription	HSMMtube	muscle
42	chr12:105585600-105598400	Strong transcription	NHDF-Ad	bronchial
43	chr12:105587400-105598400	Weak transcription	Stomach Mucosa	stomach
44	chr12:105587400-105609000	Weak transcription	Fetal Brain Male	brain
45	chr12:105587800-105598800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:105588000-105598600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:105589000-105600400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:105589000-105600400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:105589200-105597600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:105589200-105601000	Weak transcription	Hela-S3	cervix

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