Variant report

Variant	rs12320104
Chromosome Location	chr12:49920395-49920396
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49743272..49745246-chr12:49919993..49922237,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178401	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11169055	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169071	1.00[EUR][1000 genomes]
rs11830622	1.00[AMR][1000 genomes]
rs11831670	1.00[EUR][1000 genomes]
rs11834883	1.00[AMR][1000 genomes]
rs11835085	1.00[EUR][1000 genomes]
rs11836969	1.00[AMR][1000 genomes]
rs12296998	1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12298123	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12298506	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299477	1.00[EUR][1000 genomes]
rs12299743	1.00[EUR][1000 genomes]
rs12300085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12306942	1.00[ASW][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]
rs12309399	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12310046	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311319	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12311910	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12313583	1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12314348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12315746	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12315941	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12318913	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319527	1.00[EUR][1000 genomes]
rs12320434	1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320612	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321717	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13377828	1.00[AMR][1000 genomes]
rs28420769	1.00[EUR][1000 genomes]
rs57970210	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58867453	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59250711	1.00[AMR][1000 genomes]
rs59570650	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59576871	1.00[EUR][1000 genomes]
rs60254449	1.00[AMR][1000 genomes]
rs60507124	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60658484	1.00[AMR][1000 genomes]
rs61227990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7960185	1.00[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	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv1801776	chr12:49915354-49934565	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49888800-49927800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:49905200-49927000	Weak transcription	Fetal Heart	heart
3	chr12:49909600-49925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:49910600-49921600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:49911000-49923000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:49911200-49922000	Strong transcription	Fetal Intestine Large	intestine
7	chr12:49912600-49926400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr12:49912800-49922600	Strong transcription	Fetal Muscle Leg	muscle
9	chr12:49913000-49921400	Weak transcription	NHDF-Ad	bronchial
10	chr12:49913200-49921000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:49913200-49922400	Strong transcription	A549	lung
12	chr12:49913200-49923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:49913800-49922000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:49914000-49922600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:49914200-49921800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:49914200-49921800	Strong transcription	Brain Germinal Matrix	brain
17	chr12:49914400-49931400	Weak transcription	Pancreas	Pancrea
18	chr12:49914800-49921600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:49914800-49922000	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr12:49915000-49920400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:49915000-49922600	Strong transcription	GM12878-XiMat	blood
22	chr12:49915000-49925600	Weak transcription	Small Intestine	intestine
23	chr12:49915400-49922000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:49916000-49921800	Strong transcription	Stomach Smooth Muscle	stomach
25	chr12:49916200-49922200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:49916400-49920400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:49916400-49921600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:49916400-49921800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:49916400-49921800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:49916400-49922400	Strong transcription	Fetal Stomach	stomach
31	chr12:49916400-49931200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:49916600-49920400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:49916600-49920600	Strong transcription	Fetal Thymus	thymus
34	chr12:49916600-49920600	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:49916600-49922000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:49916800-49921600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:49916800-49923000	Strong transcription	Fetal Intestine Small	intestine
38	chr12:49916800-49927200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:49917600-49931200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:49917800-49920400	Strong transcription	K562	blood
41	chr12:49917800-49922000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:49918000-49920600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:49918000-49922000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:49918000-49922000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:49918000-49922000	Strong transcription	Dnd41	blood
46	chr12:49918000-49922000	Strong transcription	NH-A	brain
47	chr12:49918000-49922400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:49918200-49920600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr12:49918200-49921400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:49918200-49921800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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