Variant report

Variant	rs2530662
Chromosome Location	chr22:30033036-30033037
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29998526..30000327-chr22:30030498..30033329,2	MCF-7	breast:
2	chr22:30021415..30023125-chr22:30030680..30033150,2	K562	blood:

Variant related genes	Relation type
ENSG00000186575	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11090572	0.91[EUR][1000 genomes]
rs11704455	0.81[EUR][1000 genomes]
rs12165952	0.94[EUR][1000 genomes]
rs13054076	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800539	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2007668	0.93[JPT][hapmap]
rs2079647	0.94[JPT][hapmap]
rs2158619	0.87[CEU][hapmap]
rs2245194	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2283860	0.94[JPT][hapmap]
rs2348686	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2527334	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2527335	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2530661	0.94[JPT][hapmap]
rs2531844	0.93[JPT][hapmap]
rs2857638	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2857643	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2857646	0.86[ASN][1000 genomes]
rs2857647	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2857652	0.87[CEU][hapmap]
rs456300	0.93[JPT][hapmap]
rs465938	0.93[JPT][hapmap]
rs467812	0.93[JPT][hapmap]
rs468217	0.93[JPT][hapmap]
rs468902	0.94[JPT][hapmap]
rs4823049	0.90[EUR][1000 genomes]
rs55684603	0.82[EUR][1000 genomes]
rs56246484	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5752946	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763296	0.94[JPT][hapmap]
rs5763302	0.93[JPT][hapmap]
rs5763304	0.94[JPT][hapmap]
rs5763354	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763378	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006179	0.93[JPT][hapmap]
rs62227968	0.89[EUR][1000 genomes]
rs6361	0.93[JPT][hapmap]
rs6519793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs731647	0.91[CEU][hapmap]
rs737976	0.93[JPT][hapmap]
rs737977	0.94[JPT][hapmap]
rs756053	0.87[CEU][hapmap]
rs8140060	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs9613968	0.93[JPT][hapmap]
rs9613976	0.93[JPT][hapmap]
rs9625841	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30018400-30033400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr22:30019800-30033800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr22:30020200-30033200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr22:30020200-30033600	Weak transcription	GM12878-XiMat	blood
7	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
8	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
9	chr22:30020400-30033400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
11	chr22:30021200-30033200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr22:30021800-30041600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr22:30022000-30033400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:30022000-30037200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr22:30022000-30038400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr22:30022200-30053400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr22:30022800-30034000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr22:30023000-30037400	Weak transcription	Hela-S3	cervix
19	chr22:30023200-30038600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr22:30023600-30037800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr22:30023800-30038200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr22:30023800-30038600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr22:30024000-30034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:30024000-30037400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr22:30024200-30038200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr22:30024600-30034600	Weak transcription	HMEC	breast
27	chr22:30025800-30033600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr22:30025800-30033800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr22:30026000-30033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr22:30026200-30033800	Weak transcription	Fetal Lung	lung
31	chr22:30026400-30038000	Weak transcription	Brain Angular Gyrus	brain
32	chr22:30026800-30035200	Weak transcription	Fetal Stomach	stomach
33	chr22:30026800-30038200	Weak transcription	Spleen	Spleen
34	chr22:30026800-30055800	Weak transcription	Gastric	stomach
35	chr22:30027200-30044400	Weak transcription	Brain Substantia Nigra	brain
36	chr22:30027400-30038000	Weak transcription	Colon Smooth Muscle	Colon
37	chr22:30027600-30033400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr22:30027600-30038200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr22:30027600-30057200	Weak transcription	Brain Hippocampus Middle	brain
40	chr22:30027800-30056000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr22:30028400-30033200	Enhancers	NH-A	brain
42	chr22:30028400-30037600	Weak transcription	Fetal Intestine Large	intestine
43	chr22:30028400-30044400	Weak transcription	Pancreas	Pancrea
44	chr22:30028800-30037400	Weak transcription	HepG2	liver
45	chr22:30029600-30033400	Weak transcription	Left Ventricle	heart
46	chr22:30029600-30034800	Weak transcription	Placenta	Placenta
47	chr22:30029600-30035000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr22:30029600-30053800	Weak transcription	Esophagus	oesophagus
49	chr22:30029800-30033400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr22:30030000-30038400	Weak transcription	Primary hematopoietic stem cells	blood

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