Variant report

Variant	rs6666778
Chromosome Location	chr1:94038106-94038107
allele	C/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	chr1:94037444-94038485	A549	lung:	n/a	n/a
2	POLR2A	chr1:94037841-94038133	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:94038091-94038264	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:94037491-94038615	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:94037103-94038302	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:94037757-94038326	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:94038051-94038516	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:94037674-94038673	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:94037917-94038594	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr1:94037212-94038911	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:94037017-94038164	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:94038066-94038224	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94031670..94034762-chr1:94036485..94039973,4	K562	blood:
2	chr1:94037767..94040487-chr1:94043480..94046284,2	K562	blood:

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11576435	1.00[ASN][1000 genomes]
rs11577352	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579004	1.00[ASN][1000 genomes]
rs11579685	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580965	1.00[ASN][1000 genomes]
rs11588860	1.00[ASN][1000 genomes]
rs12066343	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073093	1.00[ASN][1000 genomes]
rs12090736	1.00[ASN][1000 genomes]
rs12732557	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739747	1.00[ASN][1000 genomes]
rs12740779	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744941	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757325	1.00[ASN][1000 genomes]
rs12760092	1.00[ASN][1000 genomes]
rs17110063	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110101	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110111	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110225	1.00[ASN][1000 genomes]
rs17110370	1.00[ASN][1000 genomes]
rs1877603	1.00[ASN][1000 genomes]
rs1877604	1.00[ASN][1000 genomes]
rs1891138	1.00[ASN][1000 genomes]
rs2818163	1.00[ASN][1000 genomes]
rs34183660	1.00[ASN][1000 genomes]
rs34423897	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34663884	1.00[ASN][1000 genomes]
rs34666525	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726063	1.00[ASN][1000 genomes]
rs35126293	1.00[ASN][1000 genomes]
rs35691338	1.00[ASN][1000 genomes]
rs35896714	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35972761	1.00[ASN][1000 genomes]
rs36115605	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3950119	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59996315	1.00[ASN][1000 genomes]
rs61780979	1.00[ASN][1000 genomes]
rs61780999	1.00[ASN][1000 genomes]
rs6660968	1.00[ASN][1000 genomes]
rs6677770	1.00[ASN][1000 genomes]
rs6679609	1.00[ASN][1000 genomes]
rs6683296	1.00[ASN][1000 genomes]
rs66966060	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67043929	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67300695	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67354439	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67511232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652539	1.00[ASN][1000 genomes]
rs72721041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511890	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514579	0.82[EUR][1000 genomes]
rs7525880	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531106	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543098	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543734	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7543763	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553185	1.00[ASN][1000 genomes]
rs7555302	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761802	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011853	chr1:93966450-94039005	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93995000-94045000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:94020800-94050600	Weak transcription	Fetal Thymus	thymus
3	chr1:94021000-94041200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:94022200-94044200	Weak transcription	Small Intestine	intestine
5	chr1:94024000-94044200	Strong transcription	HSMM	muscle
6	chr1:94024400-94040200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:94025000-94043400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:94025200-94043000	Strong transcription	Liver	Liver
9	chr1:94025200-94043000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr1:94025400-94049400	Strong transcription	Hela-S3	cervix
11	chr1:94025600-94043400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
13	chr1:94026400-94040200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:94028000-94042600	Weak transcription	Fetal Kidney	kidney
15	chr1:94029000-94040600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:94030200-94046400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:94030400-94038800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:94030800-94039600	Strong transcription	Brain Anterior Caudate	brain
19	chr1:94031000-94038600	Strong transcription	Gastric	stomach
20	chr1:94031000-94038800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:94031200-94047800	Weak transcription	GM12878-XiMat	blood
22	chr1:94031400-94042000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:94031400-94042200	Strong transcription	Ovary	ovary
24	chr1:94031800-94052400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:94032000-94041000	Strong transcription	Fetal Stomach	stomach
26	chr1:94032000-94053600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:94032200-94038200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:94032200-94040000	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:94032200-94045200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:94033000-94050000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:94033400-94038600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:94033400-94039400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:94033400-94041000	Weak transcription	Brain Germinal Matrix	brain
34	chr1:94033400-94041200	Strong transcription	NHDF-Ad	bronchial
35	chr1:94033400-94041400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:94033400-94041400	Strong transcription	NH-A	brain
37	chr1:94033400-94041600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:94033400-94043200	Strong transcription	Aorta	Aorta
39	chr1:94033400-94044800	Weak transcription	Right Atrium	heart
40	chr1:94033400-94045000	Strong transcription	NHLF	lung
41	chr1:94033400-94045000	Strong transcription	Osteobl	bone
42	chr1:94033600-94038200	Weak transcription	Psoas Muscle	Psoas
43	chr1:94033600-94041200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:94033600-94044000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:94034000-94039000	Strong transcription	Fetal Intestine Small	intestine
46	chr1:94034000-94041000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:94034000-94041200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:94034000-94041200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:94034000-94043800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr1:94034200-94038800	Strong transcription	Placenta Amnion	Placenta Amnion

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