Variant report

Variant	rs1224955
Chromosome Location	chr11:76493945-76493946
allele	A/G
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	MXI1	chr11:76492909-76496222	IMR90	lung:	n/a	chr11:76495006-76495021
2	MYC	chr11:76493742-76494852	MCF10A-Er-Src	breast:	n/a	chr11:76494160-76494170 chr11:76494703-76494719
3	TBP	chr11:76492899-76494311	Hela-S3	cervix:	n/a	n/a
4	TCF12	chr11:76493940-76494283	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:76493873-76494749	HCT-116	colon:	n/a	n/a
6	RCOR1	chr11:76493589-76494859	K562	blood:	n/a	n/a
7	TAF7	chr11:76493806-76494628	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr11:76493397-76495849	Hela-S3	cervix:	n/a	chr11:76495789-76495799 chr11:76494160-76494170 chr11:76494949-76494959 chr11:76494703-76494719
9	USF2	chr11:76493734-76494322	Hela-S3	cervix:	n/a	n/a
10	TAF1	chr11:76493845-76495826	H1-hESC	embryonic stem cell:	n/a	n/a
11	HCFC1	chr11:76493923-76494592	K562	blood:	n/a	n/a
12	SP4	chr11:76493856-76494332	H1-hESC	embryonic stem cell:	n/a	chr11:76494157-76494173
13	YY1	chr11:76493870-76494371	HCT-116	colon:	n/a	chr11:76494074-76494093 chr11:76494073-76494093 chr11:76494077-76494085
14	REST	chr11:76493885-76494296	HepG2	liver:	n/a	n/a
15	REST	chr11:76493172-76494890	A549	lung:	n/a	n/a
16	MAX	chr11:76493694-76496071	HCT-116	colon:	n/a	chr11:76495789-76495799 chr11:76494160-76494170 chr11:76494949-76494959 chr11:76494703-76494719
17	RAD21	chr11:76493913-76494306	SK-N-SH_RA	brain:	n/a	n/a
18	STAT3	chr11:76493857-76494211	MCF10A-Er-Src	breast:	n/a	chr11:76493916-76493928
19	TAF1	chr11:76493945-76495702	HepG2	liver:	n/a	n/a
20	CREB1	chr11:76493884-76494692	H1-hESC	embryonic stem cell:	n/a	n/a
21	EP300	chr11:76493687-76494448	A549	lung:	n/a	n/a
22	ZBTB7A	chr11:76493890-76494915	K562	blood:	n/a	chr11:76494843-76494854 chr11:76494842-76494853
23	YY1	chr11:76493830-76494699	HepG2	liver:	n/a	chr11:76494074-76494093 chr11:76494073-76494093 chr11:76494555-76494566 chr11:76494077-76494085
24	KAP1	chr11:76493840-76494263	U2OS	brain:	n/a	n/a
25	POLR2A	chr11:76493877-76494633	HUVEC	blood vessel:	n/a	n/a
26	RAD21	chr11:76493733-76494447	IMR90	lung:	n/a	n/a
27	POLR2A	chr11:76493824-76494932	ECC-1	luminal epithelium:	n/a	n/a
28	MAX	chr11:76493901-76495857	ECC-1	luminal epithelium:	n/a	chr11:76495789-76495799 chr11:76494160-76494170 chr11:76494949-76494959 chr11:76494703-76494719
29	ZNF143	chr11:76493863-76494569	K562	blood:	n/a	chr11:76494552-76494562
30	POLR2A	chr11:76493844-76495022	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr11:76493878-76494172	U87	brain:	n/a	n/a
32	MYC	chr11:76493882-76495791	Hela-S3	cervix:	n/a	chr11:76494160-76494170 chr11:76494949-76494959 chr11:76494703-76494719
33	NFIC	chr11:76493908-76494316	HepG2	liver:	n/a	n/a
34	POLR2A	chr11:76493870-76495794	Hela-S3	cervix:	n/a	n/a
35	STAT3	chr11:76493888-76494080	MCF10A-Er-Src	breast:	n/a	chr11:76493916-76493928
36	POLR2A	chr11:76493793-76494301	SK-N-SH	brain:	n/a	n/a
37	TAF1	chr11:76493861-76494931	ECC-1	luminal epithelium:	n/a	n/a
38	SIN3AK20	chr11:76493929-76494273	HepG2	liver:	n/a	n/a
39	MAX	chr11:76493941-76494241	H1-hESC	embryonic stem cell:	n/a	chr11:76494160-76494170
40	TCF7L2	chr11:76493874-76494870	Hela-S3	cervix:	n/a	n/a
41	YY1	chr11:76493841-76494444	SK-N-SH_RA	brain:	n/a	chr11:76494074-76494093 chr11:76494073-76494093 chr11:76494077-76494085
42	SP1	chr11:76493694-76496200	A549	lung:	n/a	chr11:76494942-76494954 chr11:76495795-76495804 chr11:76494161-76494173 chr11:76494943-76494957 chr11:76495410-76495424 chr11:76495070-76495084 chr11:76494107-76494119 chr11:76494942-76494954 chr11:76495069-76495081 chr11:76494951-76494965 chr11:76495373-76495382 chr11:76494561-76494570 chr11:76493913-76493925 chr11:76494943-76494953 chr11:76494559-76494571 chr11:76495372-76495381 chr11:76494559-76494571 chr11:76494161-76494173 chr11:76494561-76494570 chr11:76494943-76494953 chr11:76494560-76494570 chr11:76494107-76494119 chr11:76495374-76495387 chr11:76495071-76495080 chr11:76494560-76494569 chr11:76494108-76494117 chr11:76494104-76494118 chr11:76494560-76494570 chr11:76493915-76493924 chr11:76495371-76495383 chr11:76494943-76494952 chr11:76494162-76494171 chr11:76494464-76494473 chr11:76494944-76494953 chr11:76494110-76494124 chr11:76494566-76494575 chr11:76494115-76494124
43	GABPA	chr11:76493847-76494304	A549	lung:	n/a	n/a
44	TAF1	chr11:76493939-76494191	SK-N-SH	brain:	n/a	n/a
45	CREB1	chr11:76493650-76495844	HepG2	liver:	n/a	n/a
46	EP300	chr11:76493898-76494416	HepG2	liver:	n/a	n/a
47	POLR2A	chr11:76493301-76495756	Hela-S3	cervix:	n/a	n/a
48	MAX	chr11:76493666-76495309	NB4	blood:	n/a	chr11:76494160-76494170 chr11:76494949-76494959 chr11:76494703-76494719
49	NR3C1	chr11:76493914-76495724	A549	lung:	n/a	chr11:76494961-76494974 chr11:76495256-76495269
50	MYC	chr11:76493772-76495339	NB4	blood:	n/a	chr11:76494160-76494170 chr11:76494949-76494959 chr11:76494703-76494719

No.	Distal block	Cell Line	Cell type
1	chr10:105421008..105421605-chr11:76493672..76494294,2	Hela-S3	cervix:
2	chr11:76493198..76494762-chr2:42794352..42797351,2	MCF-7	breast:
3	chr11:76493700..76494528-chr2:42795376..42795876,2	Hela-S3	cervix:
4	chr11:76493164..76499691-chr11:76510608..76517041,14	MCF-7	breast:
5	chr11:76493928..76495285-chr11:85955090..85956457,46	Hela-S3	cervix:
6	chr11:76493176..76494957-chr11:76635091..76637603,2	MCF-7	breast:
7	chr1:28995044..28995565-chr11:76493618..76494135,2	Hela-S3	cervix:
8	chr11:76475599..76479568-chr11:76492254..76495485,3	K562	blood:
9	chr11:76493101..76495858-chr11:76570734..76573156,2	MCF-7	breast:
10	chr1:153963053..153963733-chr11:76493340..76494174,2	Hela-S3	cervix:
11	chr11:76492395..76495773-chr11:76745021..76748563,5	MCF-7	breast:
12	chr11:76492689..76500449-chr11:76507700..76515545,17	K562	blood:
13	chr11:76493938..76494543-chr9:113018656..113019298,2	Hela-S3	cervix:
14	chr11:72524343..72526457-chr11:76493236..76495527,2	MCF-7	breast:

Variant related genes	Relation type
TSKU	TF binding region
ENSG00000107957	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000162419	Chromatin interaction
ENSG00000261578	Chromatin interaction
ENSG00000254632	Chromatin interaction
ENSG00000078124	Chromatin interaction
ENSG00000168010	Chromatin interaction
ENSG00000136810	Chromatin interaction
ENSG00000057935	Chromatin interaction
ENSG00000198488	Chromatin interaction
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11237033	1.00[YRI][hapmap]
rs1149596	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1149597	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1149599	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1149605	0.84[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1149606	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1149608	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1149609	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1149610	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1149612	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1149614	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1149615	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1149616	0.95[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs1149617	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1149618	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs1149619	0.91[EUR][1000 genomes]
rs12577786	1.00[ASW][hapmap]
rs1664081	0.88[GIH][hapmap];0.84[MEX][hapmap]
rs34909318	1.00[EUR][1000 genomes]
rs3740776	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3740777	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733454	1.00[ASW][hapmap]
rs881930	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.83[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	nsv897931	chr11:76489673-76540708	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1224955	RP11-21L23.3	cis	Adipose Subcutaneous	GTEx
rs1224955	ACER3	cis	cerebellum	SCAN
rs1224955	POLD3	cis	parietal	SCAN
rs1224955	GUCY2EP	cis	Adipose Subcutaneous	GTEx
rs1224955	RP11-672A2.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76491600-76494000	Enhancers	Spleen	Spleen
2	chr11:76492000-76494200	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr11:76492400-76494000	Weak transcription	Gastric	stomach
4	chr11:76492600-76494000	Flanking Active TSS	Fetal Intestine Small	intestine
5	chr11:76492600-76495800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:76492600-76496400	Active TSS	Rectal Smooth Muscle	rectum
7	chr11:76492800-76494000	Weak transcription	Lung	lung
8	chr11:76493000-76494000	Flanking Active TSS	Fetal Muscle Leg	muscle
9	chr11:76493000-76494200	Flanking Active TSS	Liver	Liver
10	chr11:76493000-76494200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr11:76493200-76494000	Active TSS	Stomach Smooth Muscle	stomach
12	chr11:76493200-76494000	Flanking Active TSS	K562	blood
13	chr11:76493200-76494200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:76493200-76494400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:76493200-76494600	Active TSS	Right Atrium	heart
16	chr11:76493200-76495400	Active TSS	A549	lung
17	chr11:76493200-76495600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:76493200-76495800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:76493200-76496000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr11:76493200-76496000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr11:76493200-76496000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:76493200-76496000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:76493200-76496000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:76493200-76496000	Active TSS	Stomach Mucosa	stomach
25	chr11:76493200-76496200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr11:76493200-76496200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr11:76493200-76496200	Active TSS	Fetal Kidney	kidney
28	chr11:76493200-76496400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr11:76493400-76494000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr11:76493400-76494000	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr11:76493400-76494000	Flanking Active TSS	Fetal Lung	lung
32	chr11:76493400-76494000	Flanking Active TSS	HUVEC	blood vessel
33	chr11:76493400-76494400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr11:76493400-76495600	Active TSS	HSMM	muscle
35	chr11:76493400-76495800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:76493400-76496000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:76493400-76496000	Active TSS	Psoas Muscle	Psoas
38	chr11:76493400-76496000	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr11:76493400-76496000	Active TSS	HSMMtube	muscle
40	chr11:76493600-76494000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
41	chr11:76493600-76494000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
42	chr11:76493600-76494000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
43	chr11:76493600-76494200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
44	chr11:76493600-76494200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:76493600-76494200	Flanking Active TSS	Fetal Brain Male	brain
46	chr11:76493600-76494400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:76493600-76494400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:76493600-76494600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr11:76493600-76494600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:76493600-76494600	Active TSS	Brain Hippocampus Middle	brain

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