Variant report

Variant	rs1988640
Chromosome Location	chr6:146132005-146132006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:146131654-146136799	K562	blood:	n/a	n/a
2	POLR2A	chr6:146131923-146132152	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:146131915-146132154	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:146129217..146132069-chr6:146270897..146273160,2	K562	blood:
2	chr6:146052168..146062191-chr6:146124046..146141258,59	K562	blood:
3	chr6:146103086..146105312-chr6:146131503..146134306,2	K562	blood:
4	chr6:146131042..146132915-chr6:146157627..146159920,2	K562	blood:
5	chr6:146071292..146072870-chr6:146131842..146134542,2	K562	blood:
6	chr6:146116668..146118837-chr6:146129546..146132090,2	MCF-7	breast:
7	chr6:144411434..144414028-chr6:146131549..146134210,2	K562	blood:
8	chr6:146128343..146133564-chr6:146134211..146137578,9	MCF-7	breast:
9	chr6:146054833..146059237-chr6:146126389..146132897,8	MCF-7	breast:
10	chr6:146047378..146061811-chr6:146118130..146137627,77	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235652	TF binding region
ENSG00000112425	Chromatin interaction
ENSG00000118496	Chromatin interaction
ENSG00000235652	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000270828	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs17223456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17822170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2068029	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3891273	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4343934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4895680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4895681	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4895685	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896825	1.00[ASN][1000 genomes]
rs4896830	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4896834	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4896845	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896847	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896849	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56241331	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58588227	1.00[ASN][1000 genomes]
rs60043524	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61041405	1.00[ASN][1000 genomes]
rs6570721	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6570722	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914746	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920248	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6921551	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938028	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341315	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734166	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73568138	1.00[ASN][1000 genomes]
rs73570014	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73579478	1.00[ASN][1000 genomes]
rs9497355	1.00[ASN][1000 genomes]
rs9497366	1.00[ASN][1000 genomes]
rs9497368	1.00[ASN][1000 genomes]
rs9767028	1.00[ASN][1000 genomes]
rs999859	1.00[CEU][hapmap]
rs999860	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146105200-146134400	Weak transcription	Thymus	Thymus
2	chr6:146106000-146133600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:146110200-146135000	Weak transcription	Pancreas	Pancrea
4	chr6:146112400-146135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:146113400-146133600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:146119200-146134800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:146119400-146135000	Weak transcription	Small Intestine	intestine
8	chr6:146121200-146134600	Weak transcription	Colonic Mucosa	Colon
9	chr6:146121200-146134600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:146121400-146135000	Weak transcription	Gastric	stomach
11	chr6:146122200-146134000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:146125400-146134200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:146125800-146133400	Weak transcription	Fetal Intestine Small	intestine
14	chr6:146126600-146133000	Weak transcription	Right Atrium	heart
15	chr6:146126600-146134400	Weak transcription	Right Ventricle	heart
16	chr6:146127000-146133000	Weak transcription	Fetal Brain Male	brain
17	chr6:146127000-146133600	Weak transcription	Brain Germinal Matrix	brain
18	chr6:146127200-146134600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:146127200-146134800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:146127400-146132600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:146127400-146132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:146127400-146132800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:146127400-146133400	Weak transcription	Adipose Nuclei	Adipose
24	chr6:146127400-146133600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:146127400-146133600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:146127400-146133600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:146127400-146133600	Weak transcription	Aorta	Aorta
28	chr6:146127400-146133600	Weak transcription	Liver	Liver
29	chr6:146127400-146133600	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:146127400-146134000	Weak transcription	Fetal Intestine Large	intestine
31	chr6:146127400-146134000	Weak transcription	Fetal Kidney	kidney
32	chr6:146127400-146134200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:146127400-146134200	Weak transcription	Brain Substantia Nigra	brain
34	chr6:146127400-146134200	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:146127400-146134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:146127400-146134800	Weak transcription	Fetal Thymus	thymus
37	chr6:146127400-146135000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:146127400-146135000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:146127600-146132600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:146127600-146133000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:146127600-146133000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:146127600-146133000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:146127600-146133000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr6:146127600-146133400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:146127600-146133600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:146127600-146133600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:146127600-146133800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:146127600-146133800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:146127600-146133800	Weak transcription	Fetal Stomach	stomach
50	chr6:146127600-146133800	Weak transcription	Rectal Mucosa Donor 31	rectum

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