Variant report

Variant	rs6490105
Chromosome Location	chr12:117491201-117491202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225965395..225967471-chr12:117490550..117492773,2	MCF-7	breast:
2	chr12:117488907..117491503-chr12:117528799..117530966,2	K562	blood:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10744887	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10774899	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850742	0.84[ASN][1000 genomes]
rs10850745	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850746	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850747	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850751	0.92[CEU][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10850752	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11068299	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11068300	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11068301	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11068306	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11611741	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832441	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11834817	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11837022	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368876	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1472523	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2062528	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2173654	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291911	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs2393124	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782191	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3782192	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs4766825	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55969361	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58470318	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59756806	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6490104	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6490106	0.96[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490107	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294692	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7297303	0.82[CEU][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297917	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7953553	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956481	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7960638	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7960731	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7964668	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7964686	0.87[CEU][hapmap];0.95[EUR][1000 genomes]
rs7968761	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7968891	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7971795	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7972416	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978810	0.86[CEU][hapmap];0.96[EUR][1000 genomes]
rs9634171	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117483800-117498000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:117483800-117498200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:117483800-117498200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:117484000-117493600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:117484400-117497800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:117484800-117498200	Weak transcription	Thymus	Thymus
7	chr12:117486600-117500400	Weak transcription	Fetal Lung	lung
8	chr12:117486800-117491800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:117486800-117498800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:117487000-117493400	Weak transcription	Lung	lung
11	chr12:117487200-117492000	Weak transcription	Gastric	stomach
12	chr12:117487200-117500400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:117487400-117491400	Weak transcription	Spleen	Spleen
14	chr12:117487400-117494200	Weak transcription	A549	lung
15	chr12:117487400-117497000	Weak transcription	Ovary	ovary
16	chr12:117488200-117491400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:117488200-117491600	Enhancers	Pancreas	Pancrea
18	chr12:117488400-117491800	Enhancers	Left Ventricle	heart
19	chr12:117488600-117496800	Weak transcription	Right Atrium	heart
20	chr12:117488800-117491400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:117488800-117491600	Enhancers	GM12878-XiMat	blood
22	chr12:117488800-117491800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr12:117489000-117491400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr12:117489000-117491400	Weak transcription	Fetal Brain Male	brain
25	chr12:117489000-117492200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:117489200-117491600	Enhancers	Primary B cells from peripheral blood	blood
27	chr12:117489200-117491800	Enhancers	Fetal Thymus	thymus
28	chr12:117489200-117493600	Enhancers	Fetal Heart	heart
29	chr12:117489400-117491400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:117489400-117491600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr12:117489600-117491600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:117489600-117500400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:117489800-117491600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr12:117489800-117492200	Enhancers	Right Ventricle	heart
35	chr12:117490000-117491400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr12:117490000-117491600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr12:117490000-117491800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:117490400-117491400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr12:117490400-117491600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:117490400-117491800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr12:117490400-117493000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr12:117490400-117493200	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr12:117490600-117492800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr12:117490800-117491400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
45	chr12:117490800-117498200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:117491000-117491600	Enhancers	Stomach Mucosa	stomach
47	chr12:117491000-117491800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr12:117491000-117491800	Active TSS	Brain Anterior Caudate	brain
49	chr12:117491000-117496200	Strong transcription	Dnd41	blood
50	chr12:117491000-117498400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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