Variant report

Variant	rs2270448
Chromosome Location	chr11:65835931-65835932
allele	A/C
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	CTCF	chr11:65835722-65836017	Fibrobl	skin:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
2	CTCF	chr11:65835756-65836032	LNCaP	prostate:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
3	CTCF	chr11:65835707-65836052	GM12892	blood:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
4	CTCF	chr11:65835800-65835950	GM12871	blood:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
5	POLR2A	chr11:65835722-65835960	Hela-S3	cervix:	n/a	n/a
6	ELK1	chr11:65835835-65836005	Hela-S3	cervix:	n/a	n/a
7	HDAC2	chr11:65835653-65836036	K562	blood:	n/a	n/a
8	CTCF	chr11:65835715-65836026	MCF-7	breast:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
9	RAD21	chr11:65835562-65836088	MCF-7	breast:	n/a	chr11:65835873-65835886 chr11:65835876-65835885 chr11:65835880-65835887 chr11:65835870-65835889 chr11:65835952-65835965
10	CTCF	chr11:65835800-65835950	HCPEpiC	choroid plexus:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
11	RUNX3	chr11:65835710-65836066	GM12878	blood:	n/a	n/a
12	STAT5A	chr11:65835763-65837684	GM12878	blood:	n/a	n/a
13	CTCF	chr11:65835820-65835970	GM12801	blood:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
14	POLR2A	chr11:65835647-65836051	MCF-7	breast:	n/a	n/a
15	MXI1	chr11:65835704-65835963	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr11:65835631-65836117	A549	lung:	n/a	chr11:65835873-65835886 chr11:65835876-65835885 chr11:65835880-65835887 chr11:65835870-65835889 chr11:65835952-65835965
17	CTCF	chr11:65835820-65835970	BJ	skin:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
18	CTCF	chr11:65835820-65835970	AoAF	blood vessel:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
19	ELF1	chr11:65835786-65836061	K562	blood:	n/a	n/a
20	RAD21	chr11:65835755-65835999	GM12878	blood:	n/a	chr11:65835873-65835886 chr11:65835876-65835885 chr11:65835880-65835887 chr11:65835870-65835889 chr11:65835952-65835965
21	CTCF	chr11:65835710-65836022	SK-N-SH_RA	brain:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
22	ELF1	chr11:65835705-65836029	A549	lung:	n/a	n/a
23	CTCF	chr11:65835751-65836017	GM19239	blood:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
24	CTCF	chr11:65835800-65835950	AG10803	skin:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
25	RAD21	chr11:65835679-65836051	HepG2	liver:	n/a	chr11:65835873-65835886 chr11:65835876-65835885 chr11:65835880-65835887 chr11:65835870-65835889 chr11:65835952-65835965
26	RAD21	chr11:65835523-65836187	MCF-7	breast:	n/a	chr11:65835873-65835886 chr11:65835876-65835885 chr11:65835880-65835887 chr11:65835870-65835889 chr11:65835952-65835965
27	RAD21	chr11:65835352-65836316	SK-N-SH	brain:	n/a	chr11:65835873-65835886 chr11:65835876-65835885 chr11:65835880-65835887 chr11:65835870-65835889 chr11:65835952-65835965
28	CTCF	chr11:65835800-65835950	HCT-116	colon:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
29	MAX	chr11:65835746-65835951	K562	blood:	n/a	n/a
30	CEBPB	chr11:65835750-65835978	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr11:65835639-65836013	K562	blood:	n/a	n/a
32	ATF3	chr11:65835648-65836190	A549	lung:	n/a	n/a
33	CTCF	chr11:65835800-65835950	HFF	foreskin:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
34	SIN3A	chr11:65835721-65836022	H1-hESC	embryonic stem cell:	n/a	chr11:65835820-65835833
35	ZMIZ1	chr11:65835746-65836023	K562	blood:	n/a	n/a
36	CTCF	chr11:65835733-65836023	HepG2	liver:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
37	CTCF	chr11:65835820-65835970	AG04449	skin:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
38	CTCF	chr11:65835689-65836092	IMR90	lung:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
39	CTCF	chr11:65835800-65835950	GM12873	blood:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
40	CTCF	chr11:65835820-65835970	HAc	cerebellar:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
41	POLR2A	chr11:65835674-65835970	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr11:65835800-65835950	HBMEC	blood vessel:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
43	CTCF	chr11:65835800-65835950	HEEpiC	esophagus:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
44	CTCF	chr11:65835820-65835970	HMEC	breast:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
45	CTCF	chr11:65835753-65836031	ProgFib	skin:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
46	JUND	chr11:65835723-65836039	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr11:65835800-65835950	GM12864	blood:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
48	CTCF	chr11:65835820-65835970	RPTEC	kidney:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
49	GABPA	chr11:65835731-65836026	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr11:65835820-65835970	HRE	kidney:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885

No.	Distal block	Cell Line	Cell type
1	chr11:65654924..65660442-chr11:65834310..65838665,6	K562	blood:
2	chr11:65816864..65823380-chr11:65832037..65840391,16	MCF-7	breast:
3	chr11:65812201..65814006-chr11:65833921..65836110,2	K562	blood:
4	chr11:65656719..65659047-chr11:65835301..65837715,2	MCF-7	breast:
5	chr11:65665582..65668888-chr11:65835107..65838015,3	K562	blood:
6	chr11:65835858..65838956-chr11:66027814..66030508,4	MCF-7	breast:
7	chr11:65788482..65791914-chr11:65833749..65837289,3	MCF-7	breast:
8	chr11:65638895..65641565-chr11:65834356..65837225,2	K562	blood:
9	chr11:65756158..65757092-chr11:65835112..65836021,4	MCF-7	breast:
10	chr11:65654924..65661575-chr11:65833688..65838665,10	K562	blood:
11	chr11:65826244..65833224-chr11:65834439..65839387,11	MCF-7	breast:
12	chr11:65835414..65836385-chr11:65901737..65902639,2	MCF-7	breast:
13	chr11:65625072..65626937-chr11:65835477..65837832,2	K562	blood:
14	chr11:65835450..65836031-chr11:65902174..65902687,2	K562	blood:
15	chr11:65768121..65772581-chr11:65835630..65838620,4	MCF-7	breast:
16	chr11:65826023..65826968-chr11:65835410..65836300,2	K562	blood:
17	chr11:65773321..65775670-chr11:65834388..65836189,2	K562	blood:

Variant related genes	Relation type
PACS1	TF binding region
ENSG00000175602	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000172638	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000175229	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000254461	Chromatin interaction
ENSG00000175592	Chromatin interaction
ENSG00000238752	Chromatin interaction
ENSG00000174996	Chromatin interaction
ENSG00000175334	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10791838	0.83[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10791840	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10791841	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10791845	0.89[CEU][hapmap];0.96[GIH][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10896081	0.96[GIH][hapmap]
rs11227395	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11227415	0.96[GIH][hapmap]
rs12576969	0.93[GIH][hapmap]
rs2293121	0.90[GIH][hapmap]
rs2302883	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302884	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2430979	0.93[GIH][hapmap]
rs2452681	0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs2452682	0.93[GIH][hapmap]
rs3814744	0.96[ASN][1000 genomes]
rs3825067	0.93[GIH][hapmap]
rs4565902	0.96[ASN][1000 genomes]
rs524281	0.84[TSI][hapmap]
rs535395	0.96[GIH][hapmap]
rs547087	0.81[EUR][1000 genomes]
rs549187	0.86[TSI][hapmap]
rs6591207	0.93[GIH][hapmap]
rs6591208	0.93[GIH][hapmap]
rs7120326	0.96[GIH][hapmap]
rs7941469	0.96[GIH][hapmap]
rs7946917	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	esv3321690	chr11:65835376-65839974	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2270448	KCNK4	cis	cerebellum	SCAN
rs2270448	ROM1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65821000-65836600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:65821000-65836600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:65821200-65836000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:65821200-65836000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:65821200-65836000	Strong transcription	Fetal Intestine Large	intestine
6	chr11:65821200-65836000	Strong transcription	NHLF	lung
7	chr11:65821200-65836200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:65821200-65836600	Strong transcription	Fetal Stomach	stomach
9	chr11:65821400-65836600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:65821600-65836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:65821800-65836000	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr11:65821800-65836000	Strong transcription	Primary T cells from cord blood	blood
13	chr11:65821800-65836600	Strong transcription	Thymus	Thymus
14	chr11:65822000-65836000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:65822000-65836000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:65822000-65836000	Strong transcription	HUVEC	blood vessel
17	chr11:65822000-65836000	Strong transcription	NH-A	brain
18	chr11:65822000-65836200	Strong transcription	Hela-S3	cervix
19	chr11:65822000-65836400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:65822000-65836400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:65822000-65836400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:65822200-65836000	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr11:65822200-65836200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:65822200-65836600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr11:65822600-65836400	Strong transcription	Brain Angular Gyrus	brain
26	chr11:65828200-65836400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:65828200-65838000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:65828400-65836000	Strong transcription	HMEC	breast
29	chr11:65828400-65836600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:65828600-65836000	Strong transcription	NHEK	skin
31	chr11:65829400-65836800	Strong transcription	Dnd41	blood
32	chr11:65831800-65836600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:65831800-65836800	Weak transcription	Small Intestine	intestine
34	chr11:65832400-65836800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:65832800-65837000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr11:65833000-65836000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:65833000-65836000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr11:65833000-65836800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:65833200-65836000	Strong transcription	Fetal Intestine Small	intestine
40	chr11:65833600-65836600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:65833800-65836000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:65833800-65836600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:65833800-65836600	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr11:65833800-65836600	Genic enhancers	Primary hematopoietic stem cells	blood
45	chr11:65833800-65836800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr11:65833800-65836800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:65833800-65836800	Genic enhancers	Liver	Liver
48	chr11:65834000-65836000	Genic enhancers	GM12878-XiMat	blood
49	chr11:65834000-65836000	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr11:65834000-65836600	Genic enhancers	Duodenum Smooth Muscle	Duodenum

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