Variant report

Variant	rs12993839
Chromosome Location	chr2:55895305-55895306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55893661..55895607-chr2:55919705..55921512,2	K562	blood:

Variant related genes	Relation type
ENSG00000138035	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1013138	0.82[CHD][hapmap]
rs12618859	0.84[CHD][hapmap]
rs12623293	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12623937	0.85[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12987272	1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap]
rs12993624	0.81[CHD][hapmap]
rs12994656	0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12998664	0.84[CHD][hapmap]
rs12999966	0.81[CHB][hapmap]
rs13001452	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13004436	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13005850	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13007719	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13009649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13010217	0.84[CHD][hapmap]
rs13014123	0.93[ASN][1000 genomes]
rs13015243	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13025331	0.84[CHD][hapmap]
rs13025994	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13030396	0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1443746	0.84[CHD][hapmap]
rs1542643	0.85[AMR][1000 genomes]
rs2054729	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2291336	0.84[CHD][hapmap]
rs34400247	0.82[ASN][1000 genomes]
rs35057183	0.85[AMR][1000 genomes]
rs35861320	0.87[ASN][1000 genomes]
rs3748944	0.92[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap]
rs3748952	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3791654	0.84[CHD][hapmap]
rs3828238	0.84[CHD][hapmap]
rs6737995	0.84[CHD][hapmap]
rs878124	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][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	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
4	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
5	chr2:55864400-55919600	Weak transcription	NHLF	lung
6	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:55870800-55903600	Weak transcription	Gastric	stomach
10	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
12	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
13	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
15	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
16	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
18	chr2:55879000-55896200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:55879200-55902800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:55879400-55914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:55881200-55913000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:55881800-55898000	Weak transcription	NHDF-Ad	bronchial
24	chr2:55882200-55909600	Weak transcription	Brain Germinal Matrix	brain
25	chr2:55883000-55906800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:55883000-55919800	Weak transcription	HSMMtube	muscle
27	chr2:55883200-55906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:55883400-55906800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:55883800-55897600	Weak transcription	Brain Substantia Nigra	brain
30	chr2:55884000-55897800	Weak transcription	HMEC	breast
31	chr2:55885600-55902600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:55886000-55896000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:55887400-55896000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr2:55887600-55898400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:55887800-55900200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:55887800-55900400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:55888000-55907200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:55888400-55895600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:55888600-55899600	Weak transcription	Fetal Brain Female	brain
40	chr2:55888600-55904200	Weak transcription	Esophagus	oesophagus
41	chr2:55888800-55905200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr2:55888800-55909600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:55889800-55918400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:55890200-55902400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:55890200-55915600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:55890400-55898400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:55890400-55898400	Strong transcription	Hela-S3	cervix
48	chr2:55890400-55914200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:55891000-55896600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:55891200-55896200	Weak transcription	Right Atrium	heart

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