Variant report

Variant	rs56885420
Chromosome Location	chr12:39755509-39755510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39752339..39754010-chr12:39754627..39757326,2	K562	blood:
2	chr12:39747712..39750921-chr12:39754829..39757616,3	K562	blood:
3	chr12:39751967..39753839-chr12:39754682..39757326,2	K562	blood:
4	chr12:39755090..39757754-chr12:39764621..39766612,2	MCF-7	breast:
5	chr12:39749714..39751981-chr12:39755102..39756669,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11171568	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11171662	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11171666	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11171669	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11171682	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11171691	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11171732	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11171786	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171794	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171797	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171834	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171844	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171857	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171940	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171949	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171955	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171957	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172024	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172035	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172263	0.82[EUR][1000 genomes]
rs12227642	0.80[ASN][1000 genomes]
rs12228664	0.83[EUR][1000 genomes]
rs12231250	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12231735	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17127036	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56154721	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56326136	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57785083	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58125663	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58648215	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61101304	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7964039	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[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	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39696600-39762200	Weak transcription	Fetal Brain Male	brain
2	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
3	chr12:39699600-39760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:39718400-39756800	Weak transcription	HSMM	muscle
5	chr12:39721000-39770600	Weak transcription	Gastric	stomach
6	chr12:39722800-39767200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:39726400-39766600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:39726600-39766600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:39726600-39766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:39726600-39766800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:39726800-39762200	Weak transcription	Placenta	Placenta
12	chr12:39726800-39766600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:39727000-39755600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:39727000-39758000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:39727000-39758000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:39727000-39758200	Weak transcription	Fetal Intestine Large	intestine
17	chr12:39727000-39760600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:39727000-39761400	Weak transcription	Fetal Intestine Small	intestine
19	chr12:39727000-39762400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:39727000-39767000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
22	chr12:39735200-39761400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:39735600-39755800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:39735600-39766600	Weak transcription	HMEC	breast
25	chr12:39735600-39766600	Weak transcription	NHEK	skin
26	chr12:39737400-39766600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:39740600-39761200	Weak transcription	Brain Substantia Nigra	brain
28	chr12:39742600-39761400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:39743000-39766800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:39743200-39765800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr12:39745000-39762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:39745000-39778600	Weak transcription	Pancreas	Pancrea
33	chr12:39747800-39755800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:39748200-39764000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:39748400-39765800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:39748800-39764000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:39749000-39755800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:39749000-39764200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:39749800-39755600	Weak transcription	Psoas Muscle	Psoas
40	chr12:39749800-39761200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:39750200-39761600	Weak transcription	Small Intestine	intestine
42	chr12:39750200-39765400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:39750400-39755800	Weak transcription	Lung	lung
44	chr12:39750400-39762000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:39750600-39760000	Weak transcription	Hela-S3	cervix
46	chr12:39750600-39760400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:39750800-39762200	Weak transcription	HepG2	liver
48	chr12:39751200-39755600	Weak transcription	Brain Germinal Matrix	brain
49	chr12:39751200-39759600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:39751200-39761200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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