Variant report

Variant	rs12423697
Chromosome Location	chr12:121256834-121256835
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	chr12:121249369..121251387-chr12:121254840..121256936,2	MCF-7	breast:
2	chr12:121254206..121257153-chr12:121257780..121260885,3	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10160872	0.83[EUR][1000 genomes]
rs1027556	0.85[EUR][1000 genomes]
rs10431373	0.87[ASN][1000 genomes]
rs10431387	0.87[EUR][1000 genomes]
rs10437837	0.80[ASN][1000 genomes]
rs10437838	0.81[EUR][1000 genomes]
rs10774569	0.96[EUR][1000 genomes]
rs10774570	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10774571	0.85[EUR][1000 genomes]
rs10774573	0.83[EUR][1000 genomes]
rs10849783	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10849785	0.81[ASN][1000 genomes]
rs10849787	0.81[EUR][1000 genomes]
rs10849788	0.81[EUR][1000 genomes]
rs10849789	0.86[ASN][1000 genomes]
rs10849790	0.84[EUR][1000 genomes]
rs10849792	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10849794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849795	1.00[ASN][1000 genomes]
rs10849796	0.97[ASN][1000 genomes]
rs10849798	0.97[ASN][1000 genomes]
rs10849799	0.97[ASN][1000 genomes]
rs10849800	0.85[EUR][1000 genomes]
rs10849803	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10849805	0.85[EUR][1000 genomes]
rs10849806	0.85[EUR][1000 genomes]
rs10849808	0.87[ASN][1000 genomes]
rs10849809	0.87[ASN][1000 genomes]
rs10849810	0.85[EUR][1000 genomes]
rs10849811	0.83[EUR][1000 genomes]
rs10849812	0.81[EUR][1000 genomes]
rs10849813	0.83[EUR][1000 genomes]
rs10849814	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11065262	0.80[ASN][1000 genomes]
rs11065266	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065271	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11065276	1.00[ASN][1000 genomes]
rs11065298	0.83[EUR][1000 genomes]
rs11065313	0.81[EUR][1000 genomes]
rs11065319	0.83[EUR][1000 genomes]
rs11065320	0.83[EUR][1000 genomes]
rs11065321	0.83[EUR][1000 genomes]
rs11065322	0.83[EUR][1000 genomes]
rs12302189	0.81[ASN][1000 genomes]
rs12310161	0.83[EUR][1000 genomes]
rs2049211	0.85[EUR][1000 genomes]
rs2393718	0.96[EUR][1000 genomes]
rs3213568	0.84[EUR][1000 genomes]
rs3213569	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3809314	0.83[EUR][1000 genomes]
rs56137011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56161401	0.83[EUR][1000 genomes]
rs6489780	0.83[EUR][1000 genomes]
rs7131886	0.83[EUR][1000 genomes]
rs7139145	0.83[EUR][1000 genomes]
rs715319	0.85[EUR][1000 genomes]
rs7298639	0.83[EUR][1000 genomes]
rs7306083	0.88[EUR][1000 genomes]
rs73224325	0.87[EUR][1000 genomes]
rs73229135	1.00[ASN][1000 genomes]
rs73229156	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954254	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7965332	0.85[EUR][1000 genomes]
rs7977343	0.84[EUR][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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121211400-121260800	Weak transcription	Gastric	stomach
2	chr12:121222200-121274000	Weak transcription	Lung	lung
3	chr12:121222600-121259000	Weak transcription	Ovary	ovary
4	chr12:121222600-121260800	Weak transcription	Spleen	Spleen
5	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
6	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:121234000-121264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:121234600-121263000	Weak transcription	A549	lung
9	chr12:121236400-121259000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:121239200-121260600	Weak transcription	Right Atrium	heart
11	chr12:121240800-121260800	Weak transcription	Small Intestine	intestine
12	chr12:121241000-121261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:121241200-121258400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:121241200-121259000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:121241800-121260800	Weak transcription	Thymus	Thymus
16	chr12:121242400-121259000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:121244800-121264000	Weak transcription	Aorta	Aorta
18	chr12:121248000-121264400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:121248000-121265200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:121248200-121267200	Weak transcription	Fetal Stomach	stomach
21	chr12:121248200-121272200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:121248400-121266800	Weak transcription	Fetal Intestine Large	intestine
23	chr12:121248600-121260200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:121248600-121267200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:121248800-121259000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:121248800-121260600	Weak transcription	Fetal Thymus	thymus
27	chr12:121248800-121268600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:121248800-121270400	Weak transcription	Primary B cells from cord blood	blood
29	chr12:121248800-121271600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr12:121248800-121271800	Weak transcription	Dnd41	blood
31	chr12:121249600-121259000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:121250800-121266600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:121253000-121257000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:121253000-121260400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:121253200-121260600	Weak transcription	Fetal Kidney	kidney
36	chr12:121253800-121268600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:121254000-121258800	Weak transcription	GM12878-XiMat	blood
38	chr12:121254000-121268600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:121254800-121258000	Enhancers	Brain Hippocampus Middle	brain
40	chr12:121255000-121257200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr12:121255000-121258000	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr12:121255000-121258200	Enhancers	Brain Substantia Nigra	brain
43	chr12:121255200-121257000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:121255200-121257200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:121255200-121258000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr12:121255200-121258000	Enhancers	Brain Cingulate Gyrus	brain
47	chr12:121255200-121261600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:121255400-121257800	Enhancers	Fetal Heart	heart
49	chr12:121255800-121257800	Enhancers	Primary T cells from cord blood	blood
50	chr12:121255800-121270000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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