Variant report

Variant	rs17127072
Chromosome Location	chr12:39760452-39760453
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	chr12:39759047..39762172-chr12:39834495..39838400,6	MCF-7	breast:
2	chr12:39757176..39762110-chr12:39835391..39838507,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10506137	1.00[EUR][1000 genomes]
rs11171732	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11171794	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11171834	0.92[AFR][1000 genomes]
rs11171844	0.81[AFR][1000 genomes]
rs11171940	0.92[AFR][1000 genomes]
rs11171949	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11171955	0.92[AFR][1000 genomes]
rs11171957	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11172024	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11172035	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11172109	0.83[AFR][1000 genomes]
rs12231250	0.92[AFR][1000 genomes]
rs17120051	1.00[EUR][1000 genomes]
rs17126974	1.00[EUR][1000 genomes]
rs17126978	1.00[EUR][1000 genomes]
rs17126995	1.00[EUR][1000 genomes]
rs17127059	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17127115	0.83[AFR][1000 genomes]
rs3923944	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs4479030	1.00[EUR][1000 genomes]
rs57785083	0.92[AFR][1000 genomes]
rs58125663	0.92[AFR][1000 genomes]
rs61101304	0.92[AFR][1000 genomes]
rs61453715	0.83[AFR][1000 genomes]
rs73268350	1.00[EUR][1000 genomes]
rs9788260	1.00[YRI][hapmap];0.83[AFR][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:74 , 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	chr12:39721000-39770600	Weak transcription	Gastric	stomach
5	chr12:39722800-39767200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:39726400-39766600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:39726600-39766600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:39726600-39766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:39726600-39766800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:39726800-39762200	Weak transcription	Placenta	Placenta
11	chr12:39726800-39766600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:39727000-39760600	Weak transcription	Brain Angular Gyrus	brain
13	chr12:39727000-39761400	Weak transcription	Fetal Intestine Small	intestine
14	chr12:39727000-39762400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:39727000-39767000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
17	chr12:39735200-39761400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:39735600-39766600	Weak transcription	HMEC	breast
19	chr12:39735600-39766600	Weak transcription	NHEK	skin
20	chr12:39737400-39766600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:39740600-39761200	Weak transcription	Brain Substantia Nigra	brain
22	chr12:39742600-39761400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:39743000-39766800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:39743200-39765800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:39745000-39762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:39745000-39778600	Weak transcription	Pancreas	Pancrea
27	chr12:39748200-39764000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:39748400-39765800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:39748800-39764000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:39749000-39764200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:39749800-39761200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:39750200-39761600	Weak transcription	Small Intestine	intestine
33	chr12:39750200-39765400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:39750400-39762000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:39750800-39762200	Weak transcription	HepG2	liver
36	chr12:39751200-39761200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:39751200-39762400	Weak transcription	Adipose Nuclei	Adipose
38	chr12:39751200-39762600	Weak transcription	K562	blood
39	chr12:39751400-39770400	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:39751600-39771800	Weak transcription	Brain Anterior Caudate	brain
41	chr12:39752000-39765400	Weak transcription	Left Ventricle	heart
42	chr12:39752200-39762200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:39752200-39762600	Weak transcription	Fetal Brain Female	brain
44	chr12:39752200-39765400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:39752200-39766400	Weak transcription	Fetal Heart	heart
46	chr12:39752200-39767600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr12:39752200-39769000	Weak transcription	Ovary	ovary
48	chr12:39752200-39769200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:39753200-39760600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:39756000-39760600	Weak transcription	Lung	lung

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