Variant report

Variant	rs6503534
Chromosome Location	chr17:38191924-38191925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:38191110-38192531	A549	lung:	n/a	n/a
2	SMC3	chr17:38191323-38192365	SK-N-SH	brain:	n/a	chr17:38191337-38191347
3	POLR2A	chr17:38191918-38192146	HepG2	liver:	n/a	n/a
4	RAD21	chr17:38191226-38191924	HCT-116	colon:	n/a	n/a
5	RCOR1	chr17:38191247-38191944	IMR90	lung:	n/a	n/a
6	MXI1	chr17:38191172-38192135	IMR90	lung:	n/a	chr17:38191850-38191859
7	CTCF	chr17:38190913-38192004	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr17:38191826-38192516	SK-N-MC	brain:	n/a	n/a
9	MAZ	chr17:38191314-38192188	IMR90	lung:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38191841..38193533-chr17:38193734..38195685,2	K562	blood:
2	chr17:38183240..38186698-chr17:38191393..38193112,3	MCF-7	breast:
3	chr17:38188226..38189880-chr17:38190553..38192589,2	K562	blood:
4	chr17:38191328..38192049-chr17:38265556..38266184,3	MCF-7	breast:
5	chr17:38191456..38193795-chr17:38198203..38200454,3	K562	blood:
6	chr17:38189430..38192064-chr17:38296302..38298504,2	MCF-7	breast:
7	chr17:38191472..38192007-chr17:38242405..38243318,2	K562	blood:
8	chr17:38191285..38191947-chr17:38347680..38348560,2	K562	blood:
9	chr17:38191116..38192112-chr17:38267566..38268591,4	K562	blood:
10	chr17:38191050..38191996-chr17:38231463..38232400,5	K562	blood:
11	chr17:38191625..38193945-chr17:38255640..38257411,2	MCF-7	breast:
12	chr17:38189937..38192774-chr17:38333499..38335289,2	MCF-7	breast:
13	chr17:38191590..38193239-chr17:38198597..38200448,2	K562	blood:

No data

Variant related genes	Relation type
MED24	TF binding region
ENSG00000008838	Chromatin interaction
ENSG00000108349	Chromatin interaction
ENSG00000238793	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000126368	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1042657	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10852937	0.81[GIH][hapmap]
rs2071369	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2071370	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2227324	0.81[ASN][1000 genomes]
rs2227338	0.81[ASN][1000 genomes]
rs2302775	0.81[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2302778	0.87[ASN][1000 genomes]
rs3934886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6503532	0.81[ASN][1000 genomes]
rs7503939	0.87[ASN][1000 genomes]
rs8070452	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921651	0.83[GIH][hapmap]
rs9899955	0.82[ASN][1000 genomes]
rs9913632	0.88[JPT][hapmap];0.82[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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6503534	KRTAP4-2	cis	parietal	SCAN
rs6503534	MED24	cis	Thyroid	GTEx
rs6503534	MED24	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:38175000-38193800	Strong transcription	HepG2	liver
7	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
8	chr17:38175200-38193200	Strong transcription	Dnd41	blood
9	chr17:38175600-38193200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr17:38175600-38193200	Strong transcription	Brain Cingulate Gyrus	brain
11	chr17:38175600-38193800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:38175800-38192600	Strong transcription	Brain Germinal Matrix	brain
13	chr17:38176000-38192600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:38176000-38195400	Weak transcription	Right Atrium	heart
15	chr17:38176200-38193800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr17:38176400-38192400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:38178200-38192600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:38179000-38192600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:38180400-38192600	Strong transcription	Fetal Intestine Large	intestine
20	chr17:38180400-38193800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:38181000-38192600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr17:38181400-38192600	Strong transcription	Fetal Lung	lung
23	chr17:38181400-38193200	Strong transcription	Brain Substantia Nigra	brain
24	chr17:38181400-38193400	Strong transcription	Brain Anterior Caudate	brain
25	chr17:38181800-38192600	Strong transcription	Osteobl	bone
26	chr17:38182800-38193800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:38183000-38195600	Strong transcription	Primary T cells from cord blood	blood
28	chr17:38183200-38193800	Strong transcription	Thymus	Thymus
29	chr17:38183400-38192400	Strong transcription	Adipose Nuclei	Adipose
30	chr17:38183400-38192600	Strong transcription	NHLF	lung
31	chr17:38183400-38193200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr17:38183600-38192200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:38183600-38192200	Strong transcription	Esophagus	oesophagus
34	chr17:38183600-38192600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr17:38183600-38192800	Strong transcription	Fetal Intestine Small	intestine
36	chr17:38183600-38193200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:38183600-38193400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:38183600-38193800	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr17:38183800-38192600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr17:38183800-38192600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr17:38183800-38192600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:38183800-38192600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:38183800-38192600	Strong transcription	Lung	lung
44	chr17:38183800-38192600	Strong transcription	Spleen	Spleen
45	chr17:38183800-38193200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr17:38183800-38193200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr17:38183800-38193600	Strong transcription	K562	blood
48	chr17:38183800-38194400	Strong transcription	Placenta	Placenta
49	chr17:38183800-38195000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr17:38183800-38195600	Strong transcription	Fetal Thymus	thymus

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