Variant report

Variant	rs10201075
Chromosome Location	chr2:55548197-55548198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55547998-55548199	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55545501..55548363-chr2:55552487..55555992,3	K562	blood:
2	chr2:55545183..55549012-chr2:55745098..55746778,3	MCF-7	breast:
3	chr2:55545711..55548722-chr2:55552487..55555212,4	K562	blood:
4	chr2:55546328..55548637-chr2:55556115..55557896,2	K562	blood:

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000163001	Chromatin interaction
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10153861	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10181997	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10184362	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10186158	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10191785	0.97[AFR][1000 genomes]
rs10194658	0.95[AFR][1000 genomes]
rs10196295	0.96[AFR][1000 genomes]
rs10199332	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10202943	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10209908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10518764	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13383527	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13384739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13389151	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13389799	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13390100	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13398447	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13402277	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13404740	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13405460	1.00[EUR][1000 genomes]
rs13406929	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13408706	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13411077	1.00[EUR][1000 genomes]
rs13411257	1.00[EUR][1000 genomes]
rs13412682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13416519	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13417988	1.00[EUR][1000 genomes]
rs13419337	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13424499	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13426160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13426766	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13429863	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046801	1.00[EUR][1000 genomes]
rs17046820	1.00[EUR][1000 genomes]
rs17046828	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046829	1.00[EUR][1000 genomes]
rs17046835	1.00[EUR][1000 genomes]
rs17046837	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046881	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046898	1.00[EUR][1000 genomes]
rs17046954	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046959	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046963	1.00[EUR][1000 genomes]
rs17046964	1.00[EUR][1000 genomes]
rs17264948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2043716	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434193	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28498550	1.00[EUR][1000 genomes]
rs3861571	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3975804	0.86[AFR][1000 genomes];1.00[AMR][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	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6545486	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6704701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6707774	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6710128	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714932	1.00[EUR][1000 genomes]
rs6715991	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6717221	0.82[AFR][1000 genomes]
rs6719677	1.00[EUR][1000 genomes]
rs6726757	1.00[EUR][1000 genomes]
rs6729144	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6734415	1.00[EUR][1000 genomes]
rs6735009	1.00[EUR][1000 genomes]
rs6738517	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6741630	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6746757	0.97[AFR][1000 genomes]
rs6746983	0.97[AFR][1000 genomes]
rs6747974	0.97[AFR][1000 genomes]
rs6748541	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6754036	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6758229	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6759625	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6759763	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6759957	0.98[AFR][1000 genomes]
rs6761771	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72918961	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918964	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918965	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918972	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918975	1.00[EUR][1000 genomes]
rs72923130	1.00[EUR][1000 genomes]
rs72923156	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72923157	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72923183	1.00[EUR][1000 genomes]
rs72923187	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72923194	1.00[EUR][1000 genomes]
rs72923197	1.00[EUR][1000 genomes]
rs72924917	0.89[AMR][1000 genomes];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	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7562535	1.00[EUR][1000 genomes]
rs7577510	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7589558	1.00[EUR][1000 genomes]
rs7594907	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9309264	0.87[AFR][1000 genomes];0.89[AMR][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	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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
4	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
5	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
7	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
11	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
15	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:55524800-55549400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:55526400-55549600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
20	chr2:55535200-55549600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:55535200-55549600	Strong transcription	Dnd41	blood
22	chr2:55535400-55550200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:55536400-55548400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:55537200-55550200	Strong transcription	HSMM	muscle
25	chr2:55537400-55549600	Strong transcription	Fetal Thymus	thymus
26	chr2:55537600-55548600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr2:55537600-55550200	Strong transcription	Brain Substantia Nigra	brain
28	chr2:55537800-55554600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:55537800-55609400	Weak transcription	Lung	lung
30	chr2:55538000-55549600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:55538000-55550000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:55538600-55548600	Strong transcription	Brain Hippocampus Middle	brain
33	chr2:55538600-55548800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:55538600-55557000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:55539200-55549600	Strong transcription	Osteobl	bone
36	chr2:55539200-55567800	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:55539200-55579000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:55539200-55579000	Weak transcription	NHEK	skin
39	chr2:55539400-55553000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:55539400-55553600	Weak transcription	NHLF	lung
41	chr2:55539800-55549600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:55539800-55554400	Weak transcription	Fetal Heart	heart
43	chr2:55541400-55554200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:55541400-55564600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:55541400-55584400	Weak transcription	Spleen	Spleen
46	chr2:55541600-55553000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:55541600-55557600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:55541800-55574800	Weak transcription	Ovary	ovary
49	chr2:55542400-55559800	Weak transcription	Fetal Brain Male	brain
50	chr2:55542400-55560400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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