Variant report

Variant	rs10897533
Chromosome Location	chr11:64622869-64622870
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:189)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:189 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64618257-64624457	GM18505	blood:	n/a	n/a
2	ELK4	chr11:64622482-64622967	Hela-S3	cervix:	n/a	n/a
3	REST	chr11:64622254-64623285	A549	lung:	n/a	n/a
4	YY1	chr11:64622179-64623028	A549	lung:	n/a	n/a
5	JUN	chr11:64621896-64623360	K562	blood:	n/a	n/a
6	MAX	chr11:64622351-64622981	SK-N-SH	brain:	n/a	n/a
7	E2F6	chr11:64622005-64623215	A549	lung:	n/a	n/a
8	TEAD4	chr11:64622142-64622907	K562	blood:	n/a	n/a
9	ATF3	chr11:64622218-64623002	HCT-116	colon:	n/a	n/a
10	RUNX3	chr11:64622498-64622958	GM12878	blood:	n/a	n/a
11	MYC	chr11:64622006-64623050	A549	lung:	n/a	chr11:64622332-64622342
12	TCF12	chr11:64621943-64623065	SK-N-SH	brain:	n/a	n/a
13	YY1	chr11:64622375-64622961	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr11:64622266-64623040	ECC-1	luminal epithelium:	n/a	n/a
15	TCF7L2	chr11:64622462-64623148	PANC-1	pancreas:	n/a	n/a
16	RAD21	chr11:64622176-64622906	ECC-1	luminal epithelium:	n/a	n/a
17	PBX3	chr11:64622257-64622947	SK-N-SH	brain:	n/a	n/a
18	NFIC	chr11:64622301-64622972	ECC-1	luminal epithelium:	n/a	n/a
19	SIN3AK20	chr11:64622159-64623054	MCF-7	breast:	n/a	n/a
20	ELF1	chr11:64622215-64623218	GM12878	blood:	n/a	n/a
21	EP300	chr11:64622051-64623049	A549	lung:	n/a	n/a
22	EBF1	chr11:64622686-64622920	GM12878	blood:	n/a	chr11:64622817-64622828
23	POLR2A	chr11:64618306-64624581	GM12891	blood:	n/a	n/a
24	MAX	chr11:64622296-64622876	MCF-7	breast:	n/a	chr11:64622332-64622342
25	BCL3	chr11:64622222-64622972	A549	lung:	n/a	n/a
26	SRF	chr11:64622347-64622890	ECC-1	luminal epithelium:	n/a	n/a
27	CHD1	chr11:64622041-64623350	IMR90	lung:	n/a	n/a
28	TFAP2C	chr11:64622398-64623062	Hela-S3	cervix:	n/a	n/a
29	MAX	chr11:64622286-64622939	MCF-7	breast:	n/a	chr11:64622332-64622342
30	POLR2A	chr11:64621078-64624649	GM12891	blood:	n/a	n/a
31	FOXA2	chr11:64622170-64622877	A549	lung:	n/a	n/a
32	FOSL1	chr11:64622000-64623159	HCT-116	colon:	n/a	chr11:64622593-64622604
33	POLR2A	chr11:64622490-64622882	K562	blood:	n/a	n/a
34	YY1	chr11:64622490-64622916	ECC-1	luminal epithelium:	n/a	n/a
35	EP300	chr11:64622130-64623035	SK-N-SH	brain:	n/a	n/a
36	FOXA2	chr11:64622309-64622899	A549	lung:	n/a	n/a
37	EP300	chr11:64622298-64622991	MCF-7	breast:	n/a	n/a
38	GATA3	chr11:64622268-64623076	SK-N-SH	brain:	n/a	n/a
39	JUND	chr11:64621470-64623314	HCT-116	colon:	n/a	chr11:64622593-64622604
40	POLR2A	chr11:64622020-64624731	U87	brain:	n/a	n/a
41	GABPA	chr11:64622332-64622933	MCF-7	breast:	n/a	chr11:64622332-64622341
42	FOSL2	chr11:64622261-64622977	MCF-7	breast:	n/a	chr11:64622592-64622603
43	HDAC2	chr11:64622377-64622925	MCF-7	breast:	n/a	n/a
44	EP300	chr11:64622002-64623118	A549	lung:	n/a	n/a
45	GABPA	chr11:64622379-64622882	Hela-S3	cervix:	n/a	n/a
46	TEAD4	chr11:64622157-64622946	A549	lung:	n/a	n/a
47	E2F6	chr11:64622164-64623245	Hela-S3	cervix:	n/a	n/a
48	FOSL2	chr11:64622332-64622930	MCF-7	breast:	n/a	chr11:64622592-64622603
49	NR3C1	chr11:64622125-64622897	A549	lung:	n/a	n/a
50	POLR2A	chr11:64622078-64622973	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64544838..64547533-chr11:64621296..64624223,3	MCF-7	breast:
2	11:64620201-64626490..11:64658316-64660295	Hela-S3	cervix:
3	chr11:64544849..64546983-chr11:64621402..64625371,3	K562	blood:
4	chr11:64622436..64624370-chr11:64898964..64901159,2	MCF-7	breast:
5	chr11:64544849..64546824-chr11:64622424..64625371,2	K562	blood:
6	chr11:64622379..64623925-chr11:64879172..64881431,2	MCF-7	breast:

No data

Variant related genes	Relation type
EHD1	TF binding region
ENSG00000269038	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000207648	Chromatin interaction
ENSG00000229719	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000267804	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1211284	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12573	0.87[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12801172	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs17146413	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2007521	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077026	0.90[ASN][1000 genomes]
rs3741391	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3893108	0.99[ASN][1000 genomes]
rs3936999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3937000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs41381745	0.94[ASN][1000 genomes]
rs4930280	0.97[ASN][1000 genomes]
rs4930281	0.99[ASN][1000 genomes]
rs4930685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57851864	0.92[ASN][1000 genomes]
rs589556	0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs602347	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs607569	0.99[ASN][1000 genomes]
rs620066	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs621608	0.90[ASN][1000 genomes]
rs622611	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs635722	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs641623	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs649208	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs653225	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs654580	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs656982	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126744	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7926812	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7927560	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7943238	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7944276	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7952306	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7952567	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
2	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription 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	1071 gene(s)	inside rSNPs	diseases
5	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv897704	chr11:64584987-64701030	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
7	nsv897705	chr11:64591679-64701030	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
8	nsv897706	chr11:64591679-64721908	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
9	nsv897707	chr11:64600002-64701030	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
10	nsv897708	chr11:64602757-64695271	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
11	nsv870106	chr11:64610698-64640067	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10897533	EHD1	cis	lymphoblastoid	seeQTL
rs10897533	RPS4Y1	trans	lymphoblastoid	seeQTL
rs10897533	XIST	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64612600-64639000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:64613000-64629800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:64613000-64630600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:64617200-64627600	Genic enhancers	Fetal Intestine Small	intestine
5	chr11:64617200-64627600	Genic enhancers	NHLF	lung
6	chr11:64617600-64629600	Weak transcription	Fetal Brain Male	brain
7	chr11:64618600-64626200	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr11:64618600-64626200	Genic enhancers	Thymus	Thymus
9	chr11:64618600-64628000	Genic enhancers	Fetal Intestine Large	intestine
10	chr11:64618800-64627800	Strong transcription	Brain Germinal Matrix	brain
11	chr11:64618800-64627800	Strong transcription	Fetal Brain Female	brain
12	chr11:64618800-64627800	Genic enhancers	Fetal Muscle Leg	muscle
13	chr11:64619000-64625400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:64619000-64626600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:64619000-64627800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
16	chr11:64619000-64628200	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr11:64619200-64626200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:64619200-64626400	Genic enhancers	Fetal Thymus	thymus
19	chr11:64619200-64626400	Genic enhancers	Gastric	stomach
20	chr11:64619200-64627800	Genic enhancers	Adipose Nuclei	Adipose
21	chr11:64619200-64628000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:64619200-64628000	Genic enhancers	Spleen	Spleen
23	chr11:64619200-64630200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:64619400-64626600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:64619400-64626600	Genic enhancers	HMEC	breast
26	chr11:64619600-64623800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr11:64619600-64626200	Genic enhancers	Liver	Liver
28	chr11:64619800-64624000	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr11:64619800-64626400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:64619800-64628000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:64619800-64628000	Genic enhancers	Right Ventricle	heart
32	chr11:64619800-64632400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr11:64620000-64623200	Genic enhancers	Lung	lung
34	chr11:64620000-64624000	Strong transcription	Dnd41	blood
35	chr11:64620000-64625200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:64620400-64624600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:64620400-64625400	Enhancers	Psoas Muscle	Psoas
38	chr11:64620800-64625200	Enhancers	HUVEC	blood vessel
39	chr11:64620800-64626400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:64620800-64627800	Genic enhancers	Esophagus	oesophagus
41	chr11:64620800-64628200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:64620800-64630200	Weak transcription	Fetal Kidney	kidney
43	chr11:64621000-64623000	Strong transcription	Brain Anterior Caudate	brain
44	chr11:64621000-64623600	Genic enhancers	NHDF-Ad	bronchial
45	chr11:64621200-64624400	Genic enhancers	Primary B cells from cord blood	blood
46	chr11:64621400-64623000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:64621400-64623000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr11:64621400-64623200	Strong transcription	Brain Angular Gyrus	brain
49	chr11:64621400-64624400	Genic enhancers	Pancreas	Pancrea
50	chr11:64621400-64625200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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