Variant report

Variant	rs12373780
Chromosome Location	chr2:47253611-47253612
allele	A/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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47252397..47254046-chr2:47254810..47257644,2	K562	blood:
2	chr2:47227819..47229844-chr2:47253559..47255515,2	K562	blood:
3	chr2:47253562..47255469-chr2:47401214..47402778,2	K562	blood:
4	chr2:47252113..47260352-chr2:47399089..47405669,11	MCF-7	breast:
5	chr2:47246499..47248286-chr2:47253507..47255645,2	MCF-7	breast:
6	chr2:47252454..47254562-chr2:47258233..47260100,2	K562	blood:
7	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALM2-5	chr2:47253515-47254279	expReg_chr2_3631_-

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11125111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885389	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12373629	0.82[CHB][hapmap]
rs12373778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398062	1.00[CHB][hapmap]
rs13400315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17036135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55686748	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55830528	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56272463	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59993194	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729896	0.82[CHB][hapmap]
rs6761572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806602	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72808520	0.86[EUR][1000 genomes]
rs7578472	0.85[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv518312	chr2:47224927-47262137	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv581751	chr2:47243124-47255723	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv581752	chr2:47248111-47262137	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv521030	chr2:47249239-47255059	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv525855	chr2:47249239-47259467	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv457363	chr2:47249239-47263232	Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv581753	chr2:47249239-47263232	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv528091	chr2:47249239-47273732	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47213600-47256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:47222000-47260600	Weak transcription	Small Intestine	intestine
4	chr2:47230200-47302800	Strong transcription	Dnd41	blood
5	chr2:47232000-47265000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:47232400-47257000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:47236600-47259200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:47236600-47259200	Weak transcription	Fetal Kidney	kidney
11	chr2:47237000-47254200	Weak transcription	Ovary	ovary
12	chr2:47237000-47260400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:47238200-47253800	Strong transcription	HepG2	liver
14	chr2:47240200-47256000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:47243800-47260200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:47243800-47260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:47243800-47260800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:47243800-47261000	Weak transcription	K562	blood
19	chr2:47244000-47254200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:47244000-47256000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:47244000-47256800	Strong transcription	Osteobl	bone
22	chr2:47244000-47257200	Weak transcription	HUVEC	blood vessel
23	chr2:47244000-47258800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:47244000-47260600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:47244200-47261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:47244400-47257000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:47244600-47257000	Strong transcription	NHLF	lung
28	chr2:47244600-47258800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:47244800-47256200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:47244800-47256800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:47244800-47258800	Strong transcription	Placenta	Placenta
32	chr2:47245000-47255600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:47245800-47254400	Strong transcription	Lung	lung
34	chr2:47245800-47255000	Genic enhancers	Fetal Thymus	thymus
35	chr2:47245800-47268600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:47246000-47260400	Strong transcription	Primary B cells from cord blood	blood
37	chr2:47246000-47260800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr2:47246000-47260800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:47246000-47261800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:47246000-47283800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:47246200-47261400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:47246800-47281600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:47247000-47259800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:47247200-47257000	Genic enhancers	Fetal Muscle Trunk	muscle
45	chr2:47247400-47253800	Genic enhancers	Adipose Nuclei	Adipose
46	chr2:47247400-47254000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:47247400-47263000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:47248200-47258000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:47248600-47258000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:47248800-47254200	Strong transcription	Rectal Mucosa Donor 29	rectum

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