Variant report

Variant	rs12994656
Chromosome Location	chr2:55786739-55786740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1013138	0.85[CHB][hapmap]
rs12612227	0.81[AMR][1000 genomes]
rs12618859	0.83[CHB][hapmap];0.83[AMR][1000 genomes]
rs12623293	0.80[AMR][1000 genomes]
rs12623937	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes]
rs12986797	0.83[AMR][1000 genomes]
rs12987272	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12993839	0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12998664	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes]
rs12998780	0.84[CHB][hapmap]
rs12999966	0.81[CHB][hapmap]
rs13001452	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13004436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13007719	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13009649	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13010217	0.84[CHB][hapmap]
rs13015243	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13015744	0.90[CHB][hapmap]
rs13025331	0.84[CHB][hapmap]
rs13025994	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13030396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1542643	0.84[AMR][1000 genomes]
rs17737233	0.84[CEU][hapmap];0.84[CHB][hapmap];0.90[AMR][1000 genomes]
rs1867334	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2054729	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291336	0.85[CHB][hapmap]
rs34129478	0.81[AMR][1000 genomes]
rs34400247	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35057183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35189503	0.80[AMR][1000 genomes]
rs35255044	0.88[AMR][1000 genomes]
rs35861320	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35968359	0.93[AMR][1000 genomes]
rs3748944	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3748952	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3791654	0.83[CHB][hapmap]
rs3828238	0.85[CHB][hapmap]
rs6753530	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes]
rs878124	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
2	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
3	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
5	chr2:55760800-55788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:55761000-55788200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:55769800-55788200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:55770000-55787000	Strong transcription	Dnd41	blood
10	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
11	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:55770800-55815800	Strong transcription	Liver	Liver
13	chr2:55771200-55788000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:55771600-55788000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:55771800-55788200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:55772600-55788000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:55773200-55786800	Weak transcription	Brain Substantia Nigra	brain
18	chr2:55775200-55798000	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr2:55775800-55788000	Strong transcription	Primary hematopoietic stem cells	blood
20	chr2:55776000-55789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:55776600-55788400	Strong transcription	Primary B cells from cord blood	blood
22	chr2:55779400-55788200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:55779400-55792200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr2:55779400-55793000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:55779400-55795000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:55779400-55798200	Strong transcription	Placenta	Placenta
27	chr2:55779400-55801400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:55779600-55788200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:55779600-55793400	Strong transcription	Adipose Nuclei	Adipose
30	chr2:55779600-55797400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:55779600-55816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:55780000-55788000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:55780000-55788200	Strong transcription	Fetal Thymus	thymus
35	chr2:55780000-55791600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:55780000-55792200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:55780000-55792600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:55780000-55801400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr2:55780200-55792200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:55780600-55786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:55780600-55788000	Strong transcription	Fetal Brain Female	brain
42	chr2:55780600-55788000	Strong transcription	Fetal Stomach	stomach
43	chr2:55780800-55786800	Strong transcription	A549	lung
44	chr2:55780800-55787000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:55780800-55787600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:55781000-55792000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:55781200-55787800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:55781200-55788000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:55781200-55792000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:55781200-55794200	Strong transcription	Fetal Lung	lung

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