Variant report

Variant	rs13389799
Chromosome Location	chr2:55524012-55524013
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	chr2:55517623..55519304-chr2:55522229..55524562,2	K562	blood:
2	chr2:55517531..55519068-chr2:55523898..55526477,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10153861	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10181997	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10184362	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10186158	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10191785	0.95[AFR][1000 genomes]
rs10194658	0.93[AFR][1000 genomes]
rs10196295	0.94[AFR][1000 genomes]
rs10199332	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10201075	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10202943	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10209908	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10518764	0.86[AFR][1000 genomes]
rs13383527	1.00[EUR][1000 genomes]
rs13384739	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13389151	1.00[EUR][1000 genomes]
rs13390100	1.00[EUR][1000 genomes]
rs13398447	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13402277	1.00[EUR][1000 genomes]
rs13404740	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13405460	1.00[EUR][1000 genomes]
rs13406929	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13408706	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13411077	1.00[EUR][1000 genomes]
rs13411257	1.00[EUR][1000 genomes]
rs13412682	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13416519	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13417988	1.00[EUR][1000 genomes]
rs13419337	1.00[EUR][1000 genomes]
rs13424499	1.00[EUR][1000 genomes]
rs13426160	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13426766	1.00[EUR][1000 genomes]
rs13429863	1.00[EUR][1000 genomes]
rs17046801	1.00[EUR][1000 genomes]
rs17046820	1.00[EUR][1000 genomes]
rs17046828	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046829	1.00[EUR][1000 genomes]
rs17046835	1.00[EUR][1000 genomes]
rs17046837	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046881	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046896	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046898	1.00[EUR][1000 genomes]
rs17046954	1.00[EUR][1000 genomes]
rs17046959	1.00[EUR][1000 genomes]
rs17046963	1.00[EUR][1000 genomes]
rs17046964	1.00[EUR][1000 genomes]
rs17264948	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2043716	1.00[EUR][1000 genomes]
rs28434193	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28498550	1.00[EUR][1000 genomes]
rs3861571	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3975804	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56201519	1.00[EUR][1000 genomes]
rs57623398	1.00[EUR][1000 genomes]
rs59695161	1.00[EUR][1000 genomes]
rs60920006	1.00[EUR][1000 genomes]
rs6545485	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6545486	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6704701	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6707774	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710128	1.00[EUR][1000 genomes]
rs6714932	1.00[EUR][1000 genomes]
rs6715991	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6719677	1.00[EUR][1000 genomes]
rs6726757	1.00[EUR][1000 genomes]
rs6729144	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6734415	1.00[EUR][1000 genomes]
rs6735009	1.00[EUR][1000 genomes]
rs6738517	1.00[EUR][1000 genomes]
rs6741630	1.00[EUR][1000 genomes]
rs6746757	0.95[AFR][1000 genomes]
rs6746983	0.95[AFR][1000 genomes]
rs6747974	0.95[AFR][1000 genomes]
rs6748541	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6754036	1.00[EUR][1000 genomes]
rs6758229	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759625	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759763	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759957	0.96[AFR][1000 genomes]
rs6761771	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918961	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918964	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918965	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918972	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72918975	1.00[EUR][1000 genomes]
rs72923130	1.00[EUR][1000 genomes]
rs72923156	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923157	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923183	1.00[EUR][1000 genomes]
rs72923187	1.00[EUR][1000 genomes]
rs72923194	1.00[EUR][1000 genomes]
rs72923197	1.00[EUR][1000 genomes]
rs72924917	1.00[EUR][1000 genomes]
rs72924922	1.00[EUR][1000 genomes]
rs72927340	1.00[EUR][1000 genomes]
rs72927384	1.00[EUR][1000 genomes]
rs72927388	1.00[EUR][1000 genomes]
rs72929306	1.00[EUR][1000 genomes]
rs7561604	1.00[EUR][1000 genomes]
rs7562535	1.00[EUR][1000 genomes]
rs7577510	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7589558	1.00[EUR][1000 genomes]
rs7594907	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309264	0.81[AFR][1000 genomes];1.00[EUR][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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3431561	chr2:55523598-55525596	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
4	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
7	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
8	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
10	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
11	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:55510600-55537400	Weak transcription	Lung	lung
13	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
15	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
19	chr2:55512600-55525000	Weak transcription	Gastric	stomach
20	chr2:55512600-55546000	Weak transcription	Small Intestine	intestine
21	chr2:55513200-55525400	Strong transcription	Fetal Thymus	thymus
22	chr2:55513600-55531400	Strong transcription	Dnd41	blood
23	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:55516200-55525400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:55516400-55527800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:55518000-55524200	Strong transcription	HSMM	muscle
28	chr2:55518600-55532200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:55519400-55524400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:55519400-55529400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:55519400-55533400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
34	chr2:55520000-55538800	Weak transcription	Ovary	ovary
35	chr2:55520000-55541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:55520200-55529000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:55520200-55531600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:55520200-55539000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:55521200-55529400	Strong transcription	Osteobl	bone
42	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:55521600-55526000	Strong transcription	Hela-S3	cervix
44	chr2:55521600-55529600	Strong transcription	HepG2	liver
45	chr2:55521800-55524200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:55521800-55524200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:55521800-55525400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:55521800-55531600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:55522000-55525200	Strong transcription	Brain Germinal Matrix	brain
50	chr2:55522200-55526000	Strong transcription	Fetal Muscle Leg	muscle

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