Variant report

Variant	rs12474041
Chromosome Location	chr2:20173894-20173895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20172794..20174644-chr2:20194246..20195858,2	MCF-7	breast:
2	chr2:20173005..20174905-chr2:20250409..20253205,2	K562	blood:

Variant related genes	Relation type
ENSG00000223734	Chromatin interaction
ENSG00000068697	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12479284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731661	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731667	0.87[ASN][1000 genomes]
rs3943327	0.83[ASN][1000 genomes]
rs62109407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109410	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6734005	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs736952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587014	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
2	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
4	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
5	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
11	chr2:20133800-20176800	Weak transcription	HMEC	breast
12	chr2:20136400-20177000	Weak transcription	GM12878-XiMat	blood
13	chr2:20136400-20177200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:20136600-20177200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:20138000-20177000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:20138200-20188800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:20138600-20184800	Weak transcription	Aorta	Aorta
20	chr2:20145000-20176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:20145200-20188000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:20148400-20174600	Weak transcription	NH-A	brain
23	chr2:20149600-20174800	Weak transcription	NHDF-Ad	bronchial
24	chr2:20153200-20177400	Weak transcription	Brain Germinal Matrix	brain
25	chr2:20153200-20184400	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:20156200-20174800	Weak transcription	Liver	Liver
27	chr2:20157800-20187200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:20160600-20181200	Strong transcription	A549	lung
29	chr2:20161600-20176800	Weak transcription	HSMMtube	muscle
30	chr2:20162400-20188200	Weak transcription	Brain Substantia Nigra	brain
31	chr2:20163200-20188800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:20164200-20187800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:20164600-20187000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:20164600-20189000	Weak transcription	Placenta	Placenta
35	chr2:20164800-20189000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:20165000-20181600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:20165000-20187000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:20165000-20188400	Weak transcription	K562	blood
39	chr2:20165400-20177600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:20165400-20187600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:20165600-20174600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:20165600-20176800	Weak transcription	Thymus	Thymus
43	chr2:20165600-20177600	Weak transcription	Left Ventricle	heart
44	chr2:20165600-20184600	Weak transcription	Gastric	stomach
45	chr2:20165800-20175800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:20165800-20176600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:20165800-20179800	Weak transcription	Fetal Thymus	thymus
48	chr2:20165800-20184600	Weak transcription	Lung	lung
49	chr2:20165800-20188200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:20166000-20177000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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