Variant report

Variant	rs6428388
Chromosome Location	chr1:197112094-197112095
allele	C/T
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:7)
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	chr1:197111729-197112659	K562	blood:	n/a	n/a
2	POLR2A	chr1:197110714-197112179	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:197110354-197112735	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:197110180..197113762-chr1:197163844..197167381,3	K562	blood:
2	chr1:197063964..197065535-chr1:197110090..197112434,2	K562	blood:
3	chr1:197092500..197094237-chr1:197110834..197113696,2	K562	blood:
4	chr1:197082888..197084637-chr1:197110135..197112878,2	K562	blood:
5	chr1:197088400..197091064-chr1:197110423..197113146,2	K562	blood:
6	chr1:197080735..197084388-chr1:197109840..197112878,3	K562	blood:
7	chr1:197100050..197103962-chr1:197110434..197115621,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235748	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1537318	0.88[YRI][hapmap]
rs17514584	1.00[AMR][1000 genomes]
rs17514591	1.00[AMR][1000 genomes]
rs17514606	1.00[AMR][1000 genomes]
rs17514732	1.00[AMR][1000 genomes]
rs17514781	1.00[AMR][1000 genomes]
rs17514795	1.00[AMR][1000 genomes]
rs17514802	1.00[AMR][1000 genomes]
rs17514816	1.00[AMR][1000 genomes]
rs17549514	1.00[AMR][1000 genomes]
rs17549540	1.00[AMR][1000 genomes]
rs17549547	1.00[AMR][1000 genomes]
rs17549582	1.00[AMR][1000 genomes]
rs17549596	1.00[AMR][1000 genomes]
rs17549657	1.00[AMR][1000 genomes]
rs17549671	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17549818	1.00[AMR][1000 genomes]
rs17549859	1.00[AMR][1000 genomes]
rs17549873	1.00[AMR][1000 genomes]
rs35897746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56660423	1.00[AMR][1000 genomes]
rs56912014	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59560396	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59820773	1.00[AMR][1000 genomes]
rs5999	1.00[AMR][1000 genomes]
rs6000	1.00[AMR][1000 genomes]
rs60769813	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61117530	1.00[AMR][1000 genomes]
rs61172533	1.00[AMR][1000 genomes]
rs61249253	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61264948	1.00[AMR][1000 genomes]
rs61278057	1.00[AMR][1000 genomes]
rs62624968	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6669374	1.00[AMR][1000 genomes]
rs6669388	1.00[AMR][1000 genomes]
rs6675840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700604	1.00[AMR][1000 genomes]
rs6702338	1.00[AMR][1000 genomes]
rs6702739	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs7513644	1.00[AMR][1000 genomes]
rs7520405	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs7528827	1.00[AMR][1000 genomes]
rs7534439	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7535814	1.00[AMR][1000 genomes]
rs7539363	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs7543584	1.00[AMR][1000 genomes]
rs7545831	1.00[AMR][1000 genomes]
rs7546591	1.00[AMR][1000 genomes]
rs7554881	1.00[AMR][1000 genomes]
rs9427663	1.00[AMR][1000 genomes]
rs9727516	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
3	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
4	chr1:197073000-197115000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:197074000-197115000	Weak transcription	Fetal Brain Male	brain
6	chr1:197077000-197114200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:197095800-197114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:197100400-197112800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:197100400-197113600	Weak transcription	HSMM	muscle
10	chr1:197100600-197113000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:197100800-197114200	Weak transcription	Fetal Intestine Large	intestine
12	chr1:197101200-197113000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:197102600-197113800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:197104600-197113600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:197105400-197113600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:197106200-197112600	Strong transcription	Fetal Thymus	thymus
17	chr1:197106200-197113000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:197106400-197113400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:197106600-197113000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:197106800-197113000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:197107800-197113600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:197107800-197113800	Weak transcription	Fetal Intestine Small	intestine
23	chr1:197108000-197112400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:197108000-197113800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr1:197108000-197115000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:197108400-197113400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:197108400-197113600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:197108600-197112400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:197108600-197113600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:197108600-197113800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:197108600-197114000	Weak transcription	Fetal Stomach	stomach
32	chr1:197108600-197115000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:197108600-197115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:197109000-197112800	Genic enhancers	Hela-S3	cervix
35	chr1:197109200-197112400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:197109400-197115000	Weak transcription	HSMMtube	muscle
37	chr1:197109600-197112600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:197109600-197113600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:197109600-197113600	Active TSS	GM12878-XiMat	blood
40	chr1:197109600-197113800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:197109600-197114200	Transcr. at gene 5' and 3'	Dnd41	blood
42	chr1:197109800-197112400	Weak transcription	Fetal Lung	lung
43	chr1:197109800-197112400	Weak transcription	Osteobl	bone
44	chr1:197109800-197112600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:197109800-197113400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:197109800-197113600	Weak transcription	Fetal Brain Female	brain
47	chr1:197110200-197113400	Weak transcription	Brain Germinal Matrix	brain
48	chr1:197110200-197113600	Weak transcription	Primary T cells from cord blood	blood
49	chr1:197110400-197112800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr1:197110400-197112800	Strong transcription	A549	lung

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