Variant report

Variant	rs2412979
Chromosome Location	chr22:30580161-30580162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30578652..30582637-chr22:30590732..30593754,4	K562	blood:
2	chr22:30578196..30581092-chr22:30585737..30587811,3	MCF-7	breast:
3	chr22:30578823..30581368-chr22:30643689..30645542,2	MCF-7	breast:
4	chr22:30570903..30573377-chr22:30579968..30581667,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1122239	0.83[ASN][1000 genomes]
rs1160671	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12233358	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12483946	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs12484547	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12484740	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs12484983	0.81[CHB][hapmap]
rs12537	0.82[CHD][hapmap]
rs13053765	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13054837	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13055998	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes]
rs13056332	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056990	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13057204	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13057580	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13057733	0.82[ASN][1000 genomes]
rs13057878	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476514	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2010916	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2012308	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2106430	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2106722	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2214047	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412977	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34391152	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34420020	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34474867	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34545612	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35067150	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35539897	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35710453	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36018230	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3788422	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs4820829	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4823067	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823071	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4823080	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes]
rs4823081	0.89[EUR][1000 genomes]
rs4823082	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5753002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753007	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753013	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753015	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753019	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753020	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753022	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753027	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753028	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753029	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753030	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753046	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5753048	1.00[CEU][hapmap]
rs5763681	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs5763695	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs5763701	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs5763734	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763742	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763748	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763749	0.85[ASN][1000 genomes]
rs5763750	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763758	0.91[ASN][1000 genomes]
rs5763759	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763763	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763766	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763769	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763774	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763782	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763787	0.91[ASN][1000 genomes]
rs5763788	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763801	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763805	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763810	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763825	0.97[ASN][1000 genomes]
rs5763852	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763854	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763861	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763872	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6006393	0.92[CHB][hapmap];0.90[GIH][hapmap];0.84[ASN][1000 genomes]
rs718773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7286304	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7286681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7288576	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs739616	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs757026	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs766011	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8142101	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs916807	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs975704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];1.00[EUR][1000 genomes];1.00[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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv527188	chr22:30529741-30581722	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv524628	chr22:30575163-30581722	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30574400-30583600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr22:30575000-30583600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr22:30575400-30584400	Enhancers	Primary hematopoietic stem cells	blood
4	chr22:30575400-30584800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr22:30575600-30583400	Weak transcription	Primary T cells from cord blood	blood
6	chr22:30575600-30584600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr22:30576200-30588000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr22:30577200-30580200	Enhancers	HepG2	liver
9	chr22:30577600-30580200	Enhancers	Fetal Lung	lung
10	chr22:30577600-30589600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr22:30577600-30591400	Enhancers	A549	lung
12	chr22:30578000-30585600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr22:30578200-30584800	Weak transcription	Spleen	Spleen
14	chr22:30578400-30580800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr22:30578400-30581000	Enhancers	Dnd41	blood
16	chr22:30578400-30581400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr22:30578600-30580600	Weak transcription	Stomach Mucosa	stomach
18	chr22:30578600-30581000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr22:30578600-30581000	Weak transcription	Small Intestine	intestine
20	chr22:30578600-30581200	Weak transcription	Fetal Stomach	stomach
21	chr22:30578800-30581000	Weak transcription	Pancreas	Pancrea
22	chr22:30579000-30580200	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr22:30579000-30585400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr22:30579200-30580400	Enhancers	Osteobl	bone
25	chr22:30579200-30581200	Enhancers	HSMMtube	muscle
26	chr22:30579200-30585400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr22:30579400-30580200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr22:30579400-30580200	Enhancers	HMEC	breast
29	chr22:30579400-30581200	Enhancers	HSMM	muscle
30	chr22:30579400-30581600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr22:30579600-30580400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr22:30579600-30580600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr22:30579600-30580600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr22:30579600-30582000	Weak transcription	Fetal Intestine Large	intestine
35	chr22:30579600-30584800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr22:30579600-30591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr22:30579800-30580200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:30579800-30580200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr22:30579800-30580200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr22:30579800-30580200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr22:30579800-30581400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr22:30579800-30582800	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr22:30579800-30585400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr22:30580000-30580200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr22:30580000-30580200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr22:30580000-30580200	Enhancers	Fetal Intestine Small	intestine
47	chr22:30580000-30580400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr22:30580000-30580400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr22:30580000-30582200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr22:30580000-30584600	Weak transcription	NHLF	lung

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