Variant report

Variant	rs2408496
Chromosome Location	chr12:46650737-46650738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46518335..46521128-chr12:46649693..46651231,2	MCF-7	breast:
2	chr12:46642422..46645010-chr12:46649557..46651761,2	K562	blood:
3	chr12:46607546..46609190-chr12:46649990..46652832,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1060735	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10880947	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183420	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11504511	0.81[EUR][1000 genomes]
rs12298619	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12302984	0.82[EUR][1000 genomes]
rs12310125	0.81[EUR][1000 genomes]
rs12580583	0.81[EUR][1000 genomes]
rs1492892	0.81[EUR][1000 genomes]
rs2018424	0.81[EUR][1000 genomes]
rs2087834	0.81[EUR][1000 genomes]
rs2172398	0.81[EUR][1000 genomes]
rs2279560	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35123676	0.82[EUR][1000 genomes]
rs35497251	0.81[EUR][1000 genomes]
rs4768111	0.81[EUR][1000 genomes]
rs4768694	0.82[EUR][1000 genomes]
rs59919892	0.80[EUR][1000 genomes]
rs6582625	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7134855	0.81[EUR][1000 genomes]
rs7310869	0.82[EUR][1000 genomes]
rs7314069	0.81[EUR][1000 genomes]
rs7315493	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7316127	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7316773	0.82[EUR][1000 genomes]
rs7953659	0.81[EUR][1000 genomes]
rs7965629	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7966288	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967669	0.81[EUR][1000 genomes]
rs7970911	0.84[AMR][1000 genomes]
rs7976362	0.81[EUR][1000 genomes]
rs7980775	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46592800-46654200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:46597600-46659600	Weak transcription	Colonic Mucosa	Colon
3	chr12:46615800-46653800	Weak transcription	NH-A	brain
4	chr12:46616400-46653600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:46617000-46653000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:46618400-46653800	Weak transcription	HSMMtube	muscle
7	chr12:46622400-46650800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:46632800-46650800	Weak transcription	Brain Germinal Matrix	brain
9	chr12:46633600-46653800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:46635200-46653600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:46635600-46654000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:46635600-46660000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:46635800-46653800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:46640200-46651200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:46640400-46653600	Weak transcription	Psoas Muscle	Psoas
16	chr12:46640400-46660600	Weak transcription	Aorta	Aorta
17	chr12:46640600-46650800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:46640600-46651400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:46645000-46652000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:46645200-46659600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:46645600-46651200	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:46646000-46651200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:46646200-46653200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:46646200-46653800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:46646600-46650800	Strong transcription	NHEK	skin
26	chr12:46646600-46652200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr12:46646800-46650800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:46646800-46651000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:46647200-46650800	Weak transcription	GM12878-XiMat	blood
30	chr12:46648000-46653400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:46648200-46651000	Weak transcription	A549	lung
32	chr12:46648200-46651600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr12:46648400-46651400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr12:46648400-46654000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:46648400-46655200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:46648400-46658400	Weak transcription	HUVEC	blood vessel
37	chr12:46648600-46651000	Weak transcription	Primary T cells from cord blood	blood
38	chr12:46648600-46651600	Enhancers	Fetal Heart	heart
39	chr12:46648600-46652200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:46648600-46652200	Weak transcription	HepG2	liver
41	chr12:46648600-46652600	Weak transcription	Fetal Intestine Large	intestine
42	chr12:46648600-46653600	Weak transcription	HSMM	muscle
43	chr12:46648600-46654400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:46648600-46657400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:46648800-46650800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr12:46648800-46653400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:46648800-46656600	Weak transcription	Fetal Brain Female	brain
48	chr12:46649200-46651600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:46649200-46657800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:46649400-46651200	Weak transcription	Primary B cells from cord blood	blood

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