Variant report

Variant	rs569796
Chromosome Location	chr11:75050842-75050843
allele	C/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	CTCF	chr11:75050806-75050966	GM12878	blood:	n/a	n/a
2	CTCF	chr11:75050780-75050930	GM12870	blood:	n/a	n/a
3	CTCF	chr11:75050760-75050910	GM06990	blood:	n/a	n/a
4	CTCF	chr11:75050760-75050910	BJ	skin:	n/a	n/a
5	CTCF	chr11:75050760-75050910	HRE	kidney:	n/a	n/a
6	RAD21	chr11:75050604-75051227	HCT-116	colon:	n/a	chr11:75050885-75050897 chr11:75051034-75051048
7	RAD21	chr11:75050743-75051046	H1-hESC	embryonic stem cell:	n/a	chr11:75050885-75050897
8	CTCF	chr11:75050783-75050943	HepG2	liver:	n/a	n/a
9	CTCF	chr11:75050799-75050973	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr11:75050837-75050927	HepG2	liver:	n/a	n/a
11	CTCF	chr11:75050800-75050950	SK-N-SH_RA	brain:	n/a	n/a
12	MYC	chr11:75050512-75052176	NB4	blood:	n/a	n/a
13	CTCF	chr11:75050780-75050930	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr11:75050817-75050956	A549	lung:	n/a	n/a
15	CTCF	chr11:75050809-75050942	MCF-7	breast:	n/a	n/a
16	CTCF	chr11:75050788-75050964	MCF-7	breast:	n/a	n/a
17	CTCF	chr11:75050780-75050930	HBMEC	blood vessel:	n/a	n/a
18	CTCF	chr11:75050760-75050910	MCF-7	breast:	n/a	n/a
19	CTCF	chr11:75050760-75050910	AoAF	blood vessel:	n/a	n/a
20	RAD21	chr11:75050656-75051181	A549	lung:	n/a	chr11:75050885-75050897 chr11:75051034-75051048
21	CTCF	chr11:75050798-75050934	LNCaP	prostate:	n/a	n/a
22	CTCF	chr11:75050840-75050990	HBMEC	blood vessel:	n/a	n/a
23	RAD21	chr11:75050742-75051063	H1-hESC	embryonic stem cell:	n/a	chr11:75050885-75050897 chr11:75051034-75051048
24	CTCF	chr11:75050825-75050900	GM10266	blood:	n/a	n/a
25	CTCF	chr11:75050800-75050950	HEEpiC	esophagus:	n/a	n/a
26	RAD21	chr11:75050816-75050988	HepG2	liver:	n/a	chr11:75050885-75050897
27	SMC3	chr11:75050797-75051328	GM12878	blood:	n/a	chr11:75051218-75051232
28	CTCF	chr11:75050829-75050948	MCF-7	breast:	n/a	n/a
29	RAD21	chr11:75050616-75051145	MCF-7	breast:	n/a	chr11:75050885-75050897 chr11:75051034-75051048
30	CTCF	chr11:75050800-75050950	AG04449	skin:	n/a	n/a
31	CTCF	chr11:75050794-75051008	A549	lung:	n/a	n/a
32	CTCF	chr11:75050820-75050970	AG09319	gingival:	n/a	n/a
33	CTCF	chr11:75050780-75050930	GM12873	blood:	n/a	n/a
34	ELF1	chr11:75050795-75052267	MCF-7	breast:	n/a	chr11:75051895-75051908 chr11:75051266-75051277
35	CTCF	chr11:75050780-75050930	MCF-7	breast:	n/a	n/a
36	CTCF	chr11:75050740-75050890	HPAF	blood vessel:	n/a	n/a
37	RAD21	chr11:75050637-75051068	SK-N-SH_RA	brain:	n/a	chr11:75050885-75050897 chr11:75051034-75051048
38	CTCF	chr11:75050780-75050930	GM12878	blood:	n/a	n/a
39	CTCF	chr11:75050760-75050910	AG04450	lung:	n/a	n/a
40	CTCF	chr11:75050789-75050979	MCF-7	breast:	n/a	n/a
41	CTCF	chr11:75050720-75050870	HMF	breast:	n/a	n/a
42	CTCF	chr11:75050760-75050910	HCM	heart:	n/a	n/a
43	CTCF	chr11:75050714-75050996	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr11:75050777-75050977	K562	blood:	n/a	chr11:75050885-75050897
45	CTCF	chr11:75050780-75050930	NB4	blood:	n/a	n/a
46	TCF12	chr11:75050756-75052259	A549	lung:	n/a	chr11:75051947-75051957
47	CTCF	chr11:75050760-75050910	AG09319	gingival:	n/a	n/a
48	CTCF	chr11:75050780-75050930	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr11:75050743-75051029	A549	lung:	n/a	n/a
50	CTCF	chr11:75050817-75050940	LNCaP	prostate:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:75049020..75051039-chr11:75111036..75113038,2	MCF-7	breast:
2	chr11:75039325..75041629-chr11:75049087..75051894,3	K562	blood:
3	chr11:75050501..75052365-chr11:75057114..75058725,2	MCF-7	breast:
4	chr11:75043115..75045254-chr11:75048636..75051434,3	MCF-7	breast:
5	chr11:75050760..75054714-chr11:75085548..75088941,3	MCF-7	breast:
6	chr11:75050427..75051044-chr11:75094982..75095943,3	MCF-7	breast:
7	chr11:74986561..74988173-chr11:75048829..75051587,2	MCF-7	breast:
8	chr11:75050186..75052679-chr11:75081484..75083245,2	MCF-7	breast:
9	chr11:75050489..75051483-chr11:75095202..75095986,8	MCF-7	breast:
10	chr11:75050045..75052977-chr11:75131615..75134854,3	MCF-7	breast:
11	chr11:75047858..75058236-chr11:75058819..75065197,25	MCF-7	breast:

Variant related genes	Relation type
MIR326	TF binding region
ENSG00000149273	Chromatin interaction
ENSG00000137486	Chromatin interaction
ENSG00000206941	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2851459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475161	0.82[CEU][hapmap]
rs504683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539342	0.92[ASN][1000 genomes]
rs549085	0.90[ASN][1000 genomes]
rs561923	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs562946	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566567	0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs629991	0.82[CEU][hapmap]
rs663235	0.81[CEU][hapmap]
rs665702	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs672534	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036292	chr11:74937977-75059496	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
2	nsv1041640	chr11:74945824-75174688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv832211	chr11:74945839-75106125	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
4	nsv522447	chr11:74982939-75068767	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75035200-75051200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:75039400-75051000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr11:75039400-75060800	Enhancers	Placenta	Placenta
4	chr11:75042000-75052000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:75043200-75051600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr11:75043400-75052400	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr11:75043800-75054000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:75044200-75055400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:75044200-75055600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:75044200-75055800	Enhancers	Brain Hippocampus Middle	brain
11	chr11:75044200-75056600	Enhancers	Esophagus	oesophagus
12	chr11:75044200-75056800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:75044200-75060400	Genic enhancers	Fetal Stomach	stomach
14	chr11:75044400-75055200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:75044400-75056400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr11:75044400-75057200	Enhancers	Fetal Muscle Trunk	muscle
17	chr11:75044600-75051400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:75044600-75051800	Enhancers	Brain Cingulate Gyrus	brain
19	chr11:75044800-75051000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr11:75045000-75051000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:75045600-75051400	Enhancers	A549	lung
22	chr11:75045800-75051400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:75046200-75051000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:75046400-75051000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:75046400-75051000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:75046400-75051000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr11:75046400-75061200	Enhancers	Fetal Thymus	thymus
28	chr11:75046800-75051600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
29	chr11:75046800-75060200	Enhancers	Brain Anterior Caudate	brain
30	chr11:75046800-75061600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr11:75047000-75051400	Enhancers	Primary T cells fromperipheralblood	blood
32	chr11:75047000-75054400	Enhancers	Brain Substantia Nigra	brain
33	chr11:75047000-75059600	Enhancers	Pancreas	Pancrea
34	chr11:75047000-75061200	Enhancers	Left Ventricle	heart
35	chr11:75047000-75061200	Enhancers	Stomach Mucosa	stomach
36	chr11:75047200-75060400	Enhancers	Brain Angular Gyrus	brain
37	chr11:75047400-75051200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr11:75047400-75052200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:75047400-75052200	Enhancers	NHEK	skin
40	chr11:75047400-75055400	Enhancers	Fetal Intestine Large	intestine
41	chr11:75047600-75051000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:75047600-75051200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr11:75047600-75051400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:75047600-75051400	Enhancers	HUVEC	blood vessel
45	chr11:75047600-75054400	Enhancers	Gastric	stomach
46	chr11:75047600-75056000	Enhancers	Fetal Muscle Leg	muscle
47	chr11:75047600-75060600	Enhancers	Right Atrium	heart
48	chr11:75047800-75052200	Enhancers	Osteobl	bone
49	chr11:75047800-75053200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:75047800-75053200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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