Variant report

Variant	rs12998344
Chromosome Location	chr2:47209722-47209723
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47204388..47206742-chr2:47207490..47210493,3	K562	blood:
2	chr2:47166581..47170403-chr2:47208479..47213858,6	MCF-7	breast:
3	chr2:47201980..47204388-chr2:47208651..47211036,2	K562	blood:
4	chr2:47198362..47200774-chr2:47207735..47209827,2	K562	blood:
5	chr2:47209484..47211730-chr2:47212313..47214032,2	MCF-7	breast:
6	chr2:47188341..47190485-chr2:47209167..47212158,2	MCF-7	breast:
7	chr2:47209357..47211157-chr2:47216226..47218870,3	K562	blood:
8	chr2:47209205..47217024-chr2:47399516..47404811,13	MCF-7	breast:
9	chr2:47195860..47200774-chr2:47207735..47210386,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11893750	1.00[CEU][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13004682	1.00[CEU][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13011673	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13025013	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17036004	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1865260	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34800049	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs993848	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs993849	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv581750	chr2:47207665-47229953	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:47187800-47210200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:47195600-47210400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:47195600-47212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:47196400-47211800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:47196600-47227800	Strong transcription	Dnd41	blood
12	chr2:47198000-47209800	Weak transcription	Right Atrium	heart
13	chr2:47200200-47210000	Weak transcription	Hela-S3	cervix
14	chr2:47200800-47216400	Genic enhancers	Fetal Thymus	thymus
15	chr2:47201600-47210200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:47201600-47211800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:47201600-47213200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:47201800-47211600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:47202000-47211400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:47202000-47214800	Genic enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:47202200-47212600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:47203400-47210000	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr2:47203600-47212800	Genic enhancers	Placenta	Placenta
24	chr2:47203800-47210000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr2:47203800-47213000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:47204000-47209800	Genic enhancers	Primary hematopoietic stem cells	blood
27	chr2:47204600-47210200	Genic enhancers	Thymus	Thymus
28	chr2:47204600-47211800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:47204800-47210200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:47205800-47210200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:47206200-47211200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:47206200-47213000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:47206400-47209800	Genic enhancers	Rectal Mucosa Donor 31	rectum
34	chr2:47206400-47212000	Strong transcription	Fetal Stomach	stomach
35	chr2:47206600-47211800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:47206600-47213800	Weak transcription	Fetal Lung	lung
37	chr2:47206800-47210400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:47206800-47211200	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:47206800-47213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:47207000-47212000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:47207000-47212000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:47207000-47212000	Weak transcription	Liver	Liver
43	chr2:47207200-47210200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:47207200-47210400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:47207200-47211800	Enhancers	Pancreas	Pancrea
46	chr2:47207200-47213800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:47207200-47214200	Genic enhancers	Primary T cells from cord blood	blood
48	chr2:47207200-47214400	Weak transcription	Brain Germinal Matrix	brain
49	chr2:47207400-47210200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:47207600-47211400	Weak transcription	Aorta	Aorta

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