Variant report

Variant	rs6541068
Chromosome Location	chr1:9933281-9933282
allele	G/T
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	chr1:9933027-9933699	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:9932776..9936853-chr1:9938064..9942727,5	K562	blood:
2	chr1:9929847..9932811-chr1:9932993..9937666,4	K562	blood:
3	chr1:9931884..9936639-chr1:9967934..9971147,6	MCF-7	breast:

Variant related genes	Relation type
CTNNBIP1	TF binding region
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs4417070	0.94[ASW][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6660069	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6681118	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6686710	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6695334	0.83[ASW][hapmap]
rs72858042	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72858053	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7539650	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9904600-9935000	Weak transcription	Osteobl	bone
2	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
3	chr1:9910000-9935000	Weak transcription	NHLF	lung
4	chr1:9915800-9935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:9917800-9934400	Strong transcription	Fetal Intestine Small	intestine
6	chr1:9918600-9943800	Weak transcription	Small Intestine	intestine
7	chr1:9920200-9935200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:9921000-9934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:9921800-9934800	Weak transcription	Right Atrium	heart
10	chr1:9923800-9935200	Weak transcription	A549	lung
11	chr1:9924200-9934400	Strong transcription	Fetal Stomach	stomach
12	chr1:9924200-9935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:9924200-9935200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:9925800-9933400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:9925800-9933600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:9927600-9941800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:9928000-9934800	Weak transcription	Dnd41	blood
18	chr1:9928000-9935000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:9928000-9935000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:9928000-9935200	Weak transcription	GM12878-XiMat	blood
21	chr1:9928400-9935200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:9928400-9938000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:9929400-9933400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:9930200-9941800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:9930400-9933800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:9930400-9934800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:9930400-9935200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:9930600-9935000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:9930800-9934000	Genic enhancers	Fetal Muscle Leg	muscle
30	chr1:9930800-9934600	Weak transcription	Brain Angular Gyrus	brain
31	chr1:9930800-9942200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:9930800-9949600	Weak transcription	Fetal Lung	lung
33	chr1:9931000-9933400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:9931000-9934800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:9931000-9934800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:9931000-9934800	Weak transcription	Liver	Liver
37	chr1:9931000-9935000	Weak transcription	Primary B cells from cord blood	blood
38	chr1:9931000-9935000	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr1:9931000-9935200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:9931000-9935200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:9931200-9935200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:9931400-9933400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:9931400-9934800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:9931400-9934800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:9931600-9934800	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:9931800-9934600	Weak transcription	Brain Anterior Caudate	brain
47	chr1:9931800-9934800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:9931800-9934800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:9931800-9934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:9931800-9935000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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