Variant report

Variant	rs6489071
Chromosome Location	chr12:123025576-123025577
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123010423..123012952-chr12:123024027..123025755,2	MCF-7	breast:
2	chr12:123011807..123016958-chr12:123025504..123030876,9	K562	blood:
3	chr12:123002522..123005008-chr12:123023951..123027966,3	K562	blood:

Variant related genes	Relation type
ENSG00000111011	Chromatin interaction
ENSG00000184445	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10734924	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744275	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10744287	0.81[ASN][1000 genomes]
rs10773208	0.87[ASN][1000 genomes]
rs10773302	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10773394	0.84[ASN][1000 genomes]
rs10846978	0.84[ASN][1000 genomes]
rs10847179	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10998	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11058402	0.87[ASN][1000 genomes]
rs1392236	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1473553	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2062506	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2173628	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2342082	0.82[EUR][1000 genomes]
rs3803005	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4319547	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61954972	0.81[EUR][1000 genomes]
rs61954973	0.81[EUR][1000 genomes]
rs6416298	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6489156	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6489157	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6489158	0.82[ASN][1000 genomes]
rs6489159	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7295105	0.87[ASN][1000 genomes]
rs7295397	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307233	0.87[ASN][1000 genomes]
rs7307735	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7309390	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7314638	0.87[ASN][1000 genomes]
rs7316149	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7316734	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7397990	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7954006	0.87[ASN][1000 genomes]
rs7955203	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7959238	0.87[ASN][1000 genomes]
rs7966094	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7972728	0.85[EUR][1000 genomes]
rs9705654	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9988963	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][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	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123012400-123029400	Weak transcription	Ovary	ovary
2	chr12:123012400-123035000	Weak transcription	Lung	lung
3	chr12:123012400-123036600	Weak transcription	Esophagus	oesophagus
4	chr12:123012400-123066000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:123012400-123114000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:123012400-123117000	Weak transcription	Pancreas	Pancrea
7	chr12:123012400-123121200	Weak transcription	Aorta	Aorta
8	chr12:123012600-123031600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:123012600-123032000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:123012600-123036600	Weak transcription	Left Ventricle	heart
11	chr12:123012600-123042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:123012600-123066200	Weak transcription	Psoas Muscle	Psoas
13	chr12:123012600-123095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:123012800-123027600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:123012800-123032000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:123012800-123032000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:123012800-123036200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:123012800-123036800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:123012800-123037200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:123012800-123037600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:123012800-123042000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:123012800-123042000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:123012800-123065800	Weak transcription	Brain Substantia Nigra	brain
24	chr12:123012800-123097400	Weak transcription	Brain Angular Gyrus	brain
25	chr12:123012800-123109200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:123013000-123029400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:123013000-123029400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:123013000-123030800	Weak transcription	Adipose Nuclei	Adipose
29	chr12:123013000-123030800	Weak transcription	Fetal Lung	lung
30	chr12:123013000-123031800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:123013000-123037000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:123013000-123076400	Weak transcription	Right Ventricle	heart
33	chr12:123013000-123109200	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:123013200-123034000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:123013200-123035200	Weak transcription	Liver	Liver
36	chr12:123013200-123036200	Weak transcription	Fetal Kidney	kidney
37	chr12:123013200-123036600	Weak transcription	Spleen	Spleen
38	chr12:123013200-123037600	Weak transcription	Small Intestine	intestine
39	chr12:123013200-123045800	Strong transcription	Fetal Thymus	thymus
40	chr12:123013200-123050000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:123013200-123103000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:123013200-123112400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:123013400-123041800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:123013400-123080600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:123013400-123107400	Weak transcription	Fetal Heart	heart
46	chr12:123013400-123120600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:123013600-123028400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:123013800-123050000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:123014400-123084000	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:123014600-123027200	Weak transcription	HUVEC	blood vessel

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