Variant report

Variant	rs62415909
Chromosome Location	chr6:114270966-114270967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:114270930-114271280	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:114270880-114271394	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:114270731-114271348	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:114270822-114271968	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:114270852-114271740	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr6:114270600-114271199	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:114270844-114271325	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:114270789-114271401	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:114270756-114271354	GM12892	blood:	n/a	n/a
10	POLR2A	chr6:114268395-114272094	K562	blood:	n/a	n/a
11	POLR2A	chr6:114270857-114271826	GM12892	blood:	n/a	n/a
12	POLR2A	chr6:114270837-114271191	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:114270434..114272529-chr6:114290878..114292915,2	K562	blood:
2	chr6:114270741..114273479-chr6:114282715..114285279,2	K562	blood:
3	chr6:114270093..114272386-chr6:114275530..114278188,4	K562	blood:
4	chr6:114270093..114272386-chr6:114276092..114278188,3	K562	blood:

No data

Variant related genes	Relation type
HDAC2	TF binding region
ENSG00000196591	Chromatin interaction
ENSG00000228624	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17792118	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169506	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35598148	0.87[EUR][1000 genomes]
rs62415876	0.87[ASN][1000 genomes]
rs62415904	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62415906	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62415914	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62415915	1.00[ASN][1000 genomes]
rs62415916	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62415923	1.00[ASN][1000 genomes]
rs73548638	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744487	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488293	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488294	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3363275	chr6:114101331-114302866	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114253000-114289800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:114253400-114290600	Weak transcription	Aorta	Aorta
3	chr6:114254000-114271400	Weak transcription	Stomach Mucosa	stomach
4	chr6:114254600-114281800	Strong transcription	Dnd41	blood
5	chr6:114255400-114281600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:114255600-114276600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:114258400-114274200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:114258400-114279600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:114258600-114282600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:114258600-114291000	Weak transcription	Lung	lung
11	chr6:114258800-114279600	Strong transcription	Fetal Intestine Large	intestine
12	chr6:114258800-114281000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:114258800-114281600	Weak transcription	Gastric	stomach
14	chr6:114258800-114285600	Weak transcription	Right Ventricle	heart
15	chr6:114258800-114289800	Weak transcription	Spleen	Spleen
16	chr6:114259000-114289200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:114259400-114279800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:114259400-114281400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:114259600-114279600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr6:114259600-114281000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:114259800-114274200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:114259800-114274400	Strong transcription	HSMM	muscle
23	chr6:114259800-114280000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:114259800-114280600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:114259800-114280600	Strong transcription	Fetal Thymus	thymus
26	chr6:114259800-114280800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:114259800-114280800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:114259800-114281000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:114260000-114274400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:114260000-114280400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:114260200-114274800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:114260200-114275400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:114260200-114279600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr6:114260600-114271000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:114264800-114289800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:114265200-114280800	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:114265600-114282000	Weak transcription	Brain Substantia Nigra	brain
38	chr6:114265800-114272200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:114266000-114272800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:114266000-114283800	Weak transcription	Colonic Mucosa	Colon
41	chr6:114266000-114289600	Weak transcription	Esophagus	oesophagus
42	chr6:114266200-114277000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:114266200-114285600	Weak transcription	Psoas Muscle	Psoas
44	chr6:114266400-114271000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:114266400-114271000	Weak transcription	Fetal Intestine Small	intestine
46	chr6:114266400-114271000	Weak transcription	Fetal Stomach	stomach
47	chr6:114266400-114271600	Weak transcription	Thymus	Thymus
48	chr6:114266400-114285600	Weak transcription	Small Intestine	intestine
49	chr6:114266400-114289800	Weak transcription	Pancreas	Pancrea
50	chr6:114266600-114271000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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