Variant report

Variant	rs12468469
Chromosome Location	chr2:54786615-54786616
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54785416..54786973-chr2:54949128..54950959,2	K562	blood:
2	chr2:54341806..54344770-chr2:54784235..54787039,2	MCF-7	breast:
3	chr2:54764431..54771229-chr2:54784220..54787609,7	MCF-7	breast:
4	chr2:54342843..54345092-chr2:54785975..54787644,2	K562	blood:
5	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
6	chr2:54785770..54787299-chr2:54826149..54827905,2	K562	blood:
7	chr2:54342378..54344218-chr2:54786110..54788365,2	MCF-7	breast:
8	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237887	Chromatin interaction
ENSG00000214595	Chromatin interaction
ENSG00000228108	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10180713	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047499	0.91[EUR][1000 genomes]
rs11885703	0.86[EUR][1000 genomes]
rs11892788	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12104998	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12105792	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12467581	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12617036	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12713260	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13016942	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1367295	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1541854	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17344072	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17521078	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1864493	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2271322	0.82[EUR][1000 genomes]
rs2292356	0.91[EUR][1000 genomes]
rs2292357	0.87[EUR][1000 genomes]
rs2931463	0.82[EUR][1000 genomes]
rs2931464	0.82[EUR][1000 genomes]
rs2941583	0.83[EUR][1000 genomes]
rs2941586	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2941587	0.91[EUR][1000 genomes]
rs2941591	0.82[EUR][1000 genomes]
rs2941595	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2971877	0.91[EUR][1000 genomes]
rs2971879	0.91[EUR][1000 genomes]
rs2971883	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2971887	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3106204	0.83[EUR][1000 genomes]
rs354213	0.81[EUR][1000 genomes]
rs354228	0.80[EUR][1000 genomes]
rs354231	0.82[EUR][1000 genomes]
rs3796014	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4233952	0.82[EUR][1000 genomes]
rs4444573	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4455199	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4514917	0.80[EUR][1000 genomes]
rs4519562	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4592889	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671221	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671222	0.85[EUR][1000 genomes]
rs4671225	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671226	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671945	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671946	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671947	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671949	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671951	0.89[EUR][1000 genomes]
rs4671955	0.85[EUR][1000 genomes]
rs4671956	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671960	0.82[EUR][1000 genomes]
rs4671961	0.82[EUR][1000 genomes]
rs4990319	0.87[EUR][1000 genomes]
rs6545411	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6545413	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6545414	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6545415	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6545418	0.83[EUR][1000 genomes]
rs6545419	0.84[EUR][1000 genomes]
rs6545427	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545429	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6545434	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6704769	0.85[EUR][1000 genomes]
rs6706372	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6724590	0.83[EUR][1000 genomes]
rs6729826	0.87[EUR][1000 genomes]
rs6731661	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6732949	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734658	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6735813	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6742607	0.81[EUR][1000 genomes]
rs6746306	0.83[EUR][1000 genomes]
rs6748816	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6761369	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6761398	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7558950	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7563706	0.83[EUR][1000 genomes]
rs7589236	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7607451	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs907135	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54784000-54788200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54784200-54788400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr2:54784400-54788400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:54784600-54787800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:54784600-54787800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:54784600-54787800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:54784600-54787800	Flanking Active TSS	Fetal Muscle Leg	muscle
8	chr2:54784600-54788000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr2:54784600-54788200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:54784600-54788200	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr2:54784600-54788400	Active TSS	Thymus	Thymus
12	chr2:54784600-54788600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:54784600-54788800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:54784800-54786800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:54784800-54787000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:54784800-54787000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:54784800-54787600	Active TSS	Gastric	stomach
18	chr2:54784800-54787800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:54784800-54787800	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr2:54784800-54787800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:54784800-54787800	Active TSS	Esophagus	oesophagus
22	chr2:54784800-54788000	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr2:54784800-54788000	Active TSS	Liver	Liver
24	chr2:54784800-54788200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:54784800-54788200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:54784800-54788200	Active TSS	Lung	lung
27	chr2:54784800-54788400	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr2:54784800-54788400	Active TSS	Fetal Intestine Small	intestine
29	chr2:54784800-54788400	Active TSS	Pancreas	Pancrea
30	chr2:54784800-54788600	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr2:54784800-54789000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:54784800-54789800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:54785000-54787600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:54785000-54787600	Active TSS	Primary T cells from cord blood	blood
35	chr2:54785000-54787800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:54785000-54787800	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr2:54785000-54787800	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr2:54785000-54787800	Active TSS	NHEK	skin
39	chr2:54785000-54788000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:54785000-54788000	Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr2:54785000-54788000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr2:54785000-54788000	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr2:54785000-54788200	Active TSS	H1 Cell Line	embryonic stem cell
44	chr2:54785000-54788200	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr2:54785000-54788200	Active TSS	Primary B cells from peripheral blood	blood
46	chr2:54785000-54788200	Active TSS	Primary T cells fromperipheralblood	blood
47	chr2:54785000-54788200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:54785000-54788200	Active TSS	Fetal Thymus	thymus
49	chr2:54785000-54788200	Active TSS	Small Intestine	intestine
50	chr2:54785000-54788200	Bivalent/Poised TSS	HepG2	liver

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