Variant report

Variant	rs2288566
Chromosome Location	chr2:179474466-179474467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179462491..179465326-chr2:179473182..179475653,2	K562	blood:

Variant related genes	Relation type
ENSG00000237298	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10930832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621078	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12621108	0.86[EUR][1000 genomes]
rs1366677	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1569407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2243452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2243804	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2246932	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2252350	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2252353	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255480	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2288563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs2288568	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2288570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2303829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562832	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562835	1.00[CEU][hapmap]
rs2562837	1.00[CEU][hapmap]
rs2562841	1.00[CEU][hapmap]
rs2562843	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2562844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2562846	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2562848	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2562849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562850	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2562851	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562852	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562853	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562854	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2627038	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs2627039	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2627044	1.00[CEU][hapmap]
rs2742324	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2742328	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2742329	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2742330	1.00[CEU][hapmap]
rs2742332	1.00[CEU][hapmap]
rs2742333	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2742334	1.00[CEU][hapmap]
rs2742335	1.00[CEU][hapmap]
rs2742336	1.00[CEU][hapmap]
rs2742337	1.00[CEU][hapmap]
rs2742339	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2742340	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[EUR][1000 genomes]
rs2742341	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2742343	1.00[CEU][hapmap]
rs2742344	1.00[CEU][hapmap]
rs2742350	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2742352	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2742353	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2742354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2742355	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2742356	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2742358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3813245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3813246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3813247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55639922	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55658446	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55675869	0.86[EUR][1000 genomes]
rs55706598	0.82[EUR][1000 genomes]
rs55847232	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56018860	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56101931	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56145100	0.82[EUR][1000 genomes]
rs56214710	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56285382	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56352103	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56372427	0.82[EUR][1000 genomes]
rs72629796	0.86[EUR][1000 genomes]
rs72646834	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72646865	0.82[EUR][1000 genomes]
rs72646874	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72648257	0.90[EUR][1000 genomes]
rs72650085	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72677219	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72677228	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72677248	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1000642	chr2:179438866-179503211	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:179408000-179503000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:179428400-179478600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:179430800-179480000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:179437600-179478800	Weak transcription	Esophagus	oesophagus
6	chr2:179438200-179474800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:179438400-179518200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:179440600-179478800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:179440600-179494000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:179440600-179505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:179441400-179498800	Weak transcription	Brain Anterior Caudate	brain
12	chr2:179441600-179495000	Weak transcription	Fetal Intestine Small	intestine
13	chr2:179442000-179484200	Weak transcription	Colonic Mucosa	Colon
14	chr2:179442200-179476800	Weak transcription	Placenta	Placenta
15	chr2:179442600-179475800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:179442600-179478800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:179442800-179492000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:179442800-179493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:179444800-179484400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:179450000-179482400	Weak transcription	Small Intestine	intestine
21	chr2:179458000-179474600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:179459000-179479400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:179460800-179480200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:179461800-179480400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:179461800-179484000	Weak transcription	Fetal Brain Male	brain
26	chr2:179463800-179492000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:179464400-179477600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:179464600-179497400	Weak transcription	GM12878-XiMat	blood
29	chr2:179464800-179476200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:179464800-179477600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:179464800-179481600	Weak transcription	Dnd41	blood
32	chr2:179465600-179483600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:179465800-179481000	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:179465800-179483200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:179466200-179474600	Weak transcription	Fetal Lung	lung
36	chr2:179466200-179478600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:179466200-179480400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:179466200-179484600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:179467000-179480200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:179467200-179481800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:179468000-179486800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:179468400-179484200	Strong transcription	HSMMtube	muscle
43	chr2:179468400-179486600	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:179468400-179489200	Strong transcription	Left Ventricle	heart
45	chr2:179468400-179490400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:179468600-179480200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr2:179468600-179480400	Strong transcription	Pancreas	Pancrea
48	chr2:179468600-179484600	Strong transcription	Right Ventricle	heart
49	chr2:179468600-179486400	Strong transcription	Primary B cells from cord blood	blood
50	chr2:179468600-179486400	Strong transcription	Primary T cells fromperipheralblood	blood

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