Variant report

Variant	rs34300454
Chromosome Location	chr17:38547868-38547869
allele	C/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	chr17:38547836-38547902	K562	blood:	n/a	n/a
2	POLR2A	chr17:38547563-38547995	U87	brain:	n/a	n/a
3	POLR2A	chr17:38547657-38548349	K562	blood:	n/a	n/a
4	POLR2A	chr17:38547856-38547868	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38544588..38548116-chr17:38554882..38558246,4	K562	blood:

Variant related genes	Relation type
TOP2A	TF binding region
ENSG00000222881	TF binding region
ENSG00000131747	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10451257	1.00[TSI][hapmap]
rs10512482	1.00[EUR][1000 genomes]
rs11540720	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11867902	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs12103533	1.00[EUR][1000 genomes]
rs15685	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes]
rs16965660	1.00[EUR][1000 genomes]
rs16965669	1.00[EUR][1000 genomes]
rs16965734	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965736	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965748	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16965774	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16965778	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17616672	0.92[EUR][1000 genomes]
rs17616879	0.92[EUR][1000 genomes]
rs17617263	0.92[EUR][1000 genomes]
rs17678817	0.92[EUR][1000 genomes]
rs17678959	0.92[EUR][1000 genomes]
rs17678990	0.92[EUR][1000 genomes]
rs17679086	0.92[EUR][1000 genomes]
rs17679361	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17680217	0.92[EUR][1000 genomes]
rs17680410	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17680507	0.92[EUR][1000 genomes]
rs17680624	0.92[EUR][1000 genomes]
rs2012667	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2229773	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs28362320	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28362321	0.92[EUR][1000 genomes]
rs28526298	1.00[EUR][1000 genomes]
rs28742572	1.00[CHD][hapmap]
rs33998939	0.92[EUR][1000 genomes]
rs34270904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34530029	1.00[CHD][hapmap]
rs35783632	0.92[EUR][1000 genomes]
rs35898909	0.92[EUR][1000 genomes]
rs41283417	1.00[EUR][1000 genomes]
rs41283423	0.92[EUR][1000 genomes]
rs4134993	0.92[EUR][1000 genomes]
rs4134998	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4135005	0.92[EUR][1000 genomes]
rs4135007	0.92[EUR][1000 genomes]
rs4135012	1.00[CHD][hapmap];0.92[EUR][1000 genomes]
rs4135019	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4135021	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes]
rs4135027	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4135030	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs45612441	0.92[EUR][1000 genomes]
rs8067519	1.00[EUR][1000 genomes]
rs8071687	1.00[EUR][1000 genomes]
rs9889905	0.85[EUR][1000 genomes]
rs9891944	0.92[EUR][1000 genomes]
rs9894364	1.00[EUR][1000 genomes]
rs9894807	0.85[EUR][1000 genomes]
rs9895336	1.00[MEX][hapmap]
rs9898500	1.00[EUR][1000 genomes]
rs9899425	1.00[EUR][1000 genomes]
rs9900154	1.00[EUR][1000 genomes]
rs9903293	1.00[EUR][1000 genomes]
rs9906274	0.92[EUR][1000 genomes]
rs9909777	1.00[EUR][1000 genomes]
rs9909811	0.85[EUR][1000 genomes]
rs9910373	1.00[EUR][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	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38533600-38549600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:38536800-38562000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr17:38537200-38558600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:38538200-38557400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:38538400-38559200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr17:38539400-38565800	Weak transcription	Placenta	Placenta
7	chr17:38540200-38549000	Weak transcription	Fetal Muscle Leg	muscle
8	chr17:38540200-38553000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:38540200-38571400	Strong transcription	Fetal Thymus	thymus
10	chr17:38540400-38553000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:38541400-38549600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr17:38541400-38551000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:38541800-38559000	Strong transcription	A549	lung
14	chr17:38542000-38555000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:38542000-38556800	Weak transcription	Fetal Lung	lung
16	chr17:38542200-38571600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr17:38542400-38549200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr17:38542400-38551200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr17:38542400-38560400	Strong transcription	Dnd41	blood
20	chr17:38542600-38566000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:38542600-38566400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:38542600-38571800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:38543000-38557000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr17:38543000-38566000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr17:38543200-38553400	Strong transcription	HMEC	breast
26	chr17:38543200-38559000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:38543200-38571000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr17:38543400-38571000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr17:38543400-38571400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:38543400-38571800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:38543600-38551200	Strong transcription	NHEK	skin
32	chr17:38543800-38551400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:38543800-38555200	Strong transcription	HUVEC	blood vessel
34	chr17:38543800-38566000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:38543800-38566400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:38543800-38566400	Weak transcription	Fetal Heart	heart
37	chr17:38544000-38549800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr17:38544000-38553400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr17:38544000-38553800	Strong transcription	GM12878-XiMat	blood
40	chr17:38544000-38561200	Strong transcription	Hela-S3	cervix
41	chr17:38544000-38566600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr17:38544000-38566800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr17:38544000-38569800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr17:38544000-38570200	Strong transcription	HepG2	liver
45	chr17:38544000-38571800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:38544200-38549800	Strong transcription	NH-A	brain
47	chr17:38544200-38561400	Strong transcription	Osteobl	bone
48	chr17:38544200-38567000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr17:38544400-38549000	Strong transcription	HSMM	muscle
50	chr17:38544400-38553200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links