Variant report

Variant	rs11555254
Chromosome Location	chr17:38175866-38175867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr17:38175457-38176032	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr17:38175820-38175970	BE2_C	brain:	n/a	n/a
3	MYC	chr17:38174868-38175869	MCF10A-Er-Src	breast:	n/a	chr17:38174944-38174954
4	CTCF	chr17:38175760-38175910	BJ	skin:	n/a	n/a
5	MXI1	chr17:38175320-38176027	IMR90	lung:	n/a	n/a
6	CTCF	chr17:38175800-38175950	BJ	skin:	n/a	n/a
7	CTCF	chr17:38175720-38175870	HUVEC	blood vessel:	n/a	n/a
8	STAT3	chr17:38175456-38176048	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr17:38175406-38176036	MCF10A-Er-Src	breast:	n/a	n/a
10	JUN	chr17:38175489-38175881	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr17:38175797-38175875	Fibrobl	skin:	n/a	n/a
12	CTCF	chr17:38175800-38175950	A549	lung:	n/a	n/a
13	CTCF	chr17:38175840-38175990	NHDF-neo	bronchial:	n/a	n/a
14	POLR2A	chr17:38175260-38175923	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr17:38170916-38176213	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr17:38173937-38175874	MCF10A-Er-Src	breast:	n/a	chr17:38174947-38174956
17	POLR2A	chr17:38170766-38176716	U87	brain:	n/a	n/a
18	CTCF	chr17:38175760-38175910	AoAF	blood vessel:	n/a	n/a
19	POLR2A	chr17:38170628-38176722	U87	brain:	n/a	n/a
20	CTCF	chr17:38175840-38175990	AG04450	lung:	n/a	n/a
21	CTCF	chr17:38175820-38175970	HAc	cerebellar:	n/a	n/a
22	CEBPB	chr17:38175480-38175904	IMR90	lung:	n/a	n/a
23	POLR2A	chr17:38175414-38176036	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr17:38175622-38175941	K562	blood:	n/a	n/a
25	CTCF	chr17:38175720-38175870	HAc	cerebellar:	n/a	n/a
26	POLR2A	chr17:38173854-38176132	HUVEC	blood vessel:	n/a	n/a
27	CTCF	chr17:38175748-38175895	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOS	chr17:38175475-38175868	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr17:38174089-38176121	HUVEC	blood vessel:	n/a	n/a
30	MYC	chr17:38175207-38175870	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr17:38171205-38176070	U87	brain:	n/a	n/a
32	POLR2A	chr17:38173976-38176162	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr17:38175780-38175930	HPAF	blood vessel:	n/a	n/a
34	CTCF	chr17:38175820-38175970	GM12873	blood:	n/a	n/a
35	MYC	chr17:38175440-38175905	HUVEC	blood vessel:	n/a	n/a
36	STAT3	chr17:38175465-38175884	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38174242..38176838-chr17:38278779..38280861,2	MCF-7	breast:
2	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:
3	chr17:38174715..38177590-chr17:38209751..38212777,3	K562	blood:
4	chr17:38175071..38177613-chr17:38178105..38180812,3	MCF-7	breast:
5	chr17:38174842..38178903-chr17:38208625..38211251,3	K562	blood:
6	chr17:38172859..38176802-chr17:38178682..38181500,4	K562	blood:
7	chr17:38141745..38144493-chr17:38173834..38176591,2	MCF-7	breast:
8	chr17:38171100..38173173-chr17:38173231..38176436,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265799	TF binding region
ENSG00000188895	Chromatin interaction
ENSG00000238793	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000108342	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11078932	0.98[EUR][1000 genomes]
rs11555255	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654473	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655584	1.00[CHD][hapmap]
rs2012	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs2227316	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227325	1.00[ASN][1000 genomes]
rs2827	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36006659	1.00[EUR][1000 genomes]
rs3859188	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs58212353	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6503529	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7217241	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217694	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222093	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7222556	0.98[EUR][1000 genomes]
rs7224260	0.94[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225565	1.00[EUR][1000 genomes]
rs8068076	1.00[EUR][1000 genomes]
rs8073732	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080546	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9894543	0.93[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9912981	0.98[EUR][1000 genomes]
rs9913535	0.98[EUR][1000 genomes]
rs9916279	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11555254	MED24	cis	Thyroid	GTEx
rs11555254	SRCIN1	cis	cerebellum	SCAN
rs11555254	KRTAP4-2	cis	parietal	SCAN
rs11555254	GSDMB	cis	parietal	SCAN
rs11555254	CDC6	cis	cerebellum	SCAN
rs11555254	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	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:38170000-38176000	Enhancers	Ovary	ovary
6	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr17:38170400-38177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
10	chr17:38171600-38176800	Weak transcription	Hela-S3	cervix
11	chr17:38172200-38176000	Enhancers	HUVEC	blood vessel
12	chr17:38172400-38178400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr17:38172800-38176800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:38173000-38176600	Genic enhancers	Fetal Stomach	stomach
15	chr17:38173000-38179600	Strong transcription	Fetal Intestine Small	intestine
16	chr17:38173000-38181400	Weak transcription	Fetal Kidney	kidney
17	chr17:38173200-38176800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:38173600-38176600	Enhancers	Psoas Muscle	Psoas
21	chr17:38173600-38180200	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr17:38173600-38180400	Genic enhancers	NHLF	lung
23	chr17:38173600-38182000	Strong transcription	Thymus	Thymus
24	chr17:38173800-38176000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr17:38173800-38176000	Enhancers	Right Atrium	heart
26	chr17:38173800-38176800	Enhancers	Stomach Mucosa	stomach
27	chr17:38173800-38179400	Strong transcription	Fetal Intestine Large	intestine
28	chr17:38173800-38179800	Genic enhancers	Spleen	Spleen
29	chr17:38173800-38180600	Strong transcription	Brain Anterior Caudate	brain
30	chr17:38173800-38181400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr17:38173800-38181800	Strong transcription	Primary T cells from cord blood	blood
32	chr17:38173800-38182400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr17:38174000-38176000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
34	chr17:38174000-38176000	Weak transcription	Aorta	Aorta
35	chr17:38174000-38176600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr17:38174000-38178200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr17:38174200-38176000	Enhancers	HSMMtube	muscle
40	chr17:38174200-38176600	Genic enhancers	Lung	lung
41	chr17:38174200-38179600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:38174200-38180400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr17:38174200-38180800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr17:38174200-38183200	Strong transcription	Placenta	Placenta
45	chr17:38174200-38183400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:38174200-38183400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:38174200-38187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:38174400-38176000	Enhancers	NH-A	brain
49	chr17:38174400-38176600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:38174400-38179200	Strong transcription	Pancreas	Pancrea

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