Variant report

Variant	rs2180974
Chromosome Location	chr11:35199880-35199881
allele	C/T
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	POLR2A	chr11:35199775-35200191	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:35199365-35200368	GM12891	blood:	n/a	n/a
3	POLR2A	chr11:35197745-35203204	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr11:35199354-35200069	GM12891	blood:	n/a	n/a
5	POLR2A	chr11:35197908-35203212	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr11:35199761-35200095	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:35199631-35200196	GM12891	blood:	n/a	n/a
8	POLR2A	chr11:35197880-35203195	U87	brain:	n/a	n/a
9	POLR2A	chr11:35197784-35203201	U87	brain:	n/a	n/a
10	POLR2A	chr11:35198969-35201534	GM12892	blood:	n/a	n/a
11	POLR2A	chr11:35199437-35201574	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:35198885-35203035	GM12892	blood:	n/a	n/a
13	CEBPB	chr11:35199634-35199886	Hela-S3	cervix:	n/a	chr11:35199758-35199769 chr11:35199757-35199768
14	CEBPB	chr11:35199603-35199942	IMR90	lung:	n/a	chr11:35199758-35199769 chr11:35199757-35199768
15	POLR2A	chr11:35198835-35203167	GM12891	blood:	n/a	n/a
16	CEBPB	chr11:35199588-35199948	HepG2	liver:	n/a	chr11:35199758-35199769 chr11:35199757-35199768
17	MYC	chr11:35199631-35200783	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr11:35198820-35200322	GM12892	blood:	n/a	n/a
19	STAT3	chr11:35199798-35200886	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr11:35199353-35200093	Hela-S3	cervix:	n/a	n/a
21	MYC	chr11:35199606-35199929	MCF10A-Er-Src	breast:	n/a	n/a
22	GTF2F1	chr11:35199860-35199888	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr11:35199668-35202263	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:35199876-35199993	ProgFib	skin:	n/a	n/a
25	POLR2A	chr11:35198801-35203213	U87	brain:	n/a	n/a
26	CEBPB	chr11:35199596-35199936	A549	lung:	n/a	chr11:35199758-35199769 chr11:35199757-35199768

No.	Distal block	Cell Line	Cell type
1	chr11:35193443..35196303-chr11:35198924..35201669,2	MCF-7	breast:
2	chr11:35186608..35189447-chr11:35199235..35201624,2	MCF-7	breast:
3	chr11:35199491..35202638-chr11:35207456..35210593,3	MCF-7	breast:

Variant related genes	Relation type
CD44	TF binding region
ENSG00000026508	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs353613	0.83[ASN][1000 genomes]
rs353629	0.80[ASN][1000 genomes]
rs353630	0.88[ASN][1000 genomes]
rs353637	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353640	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353643	0.88[ASN][1000 genomes]
rs353646	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353648	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794105	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6484769	0.92[AFR][1000 genomes];0.97[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	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2758263	chr11:35029933-35226784	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2759818	chr11:35029933-35238578	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv541001	chr11:35053717-35224624	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv2757437	chr11:35067482-35238578	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv2752912	chr11:35074167-35238578	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv508623	chr11:35094933-35203363	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv541002	chr11:35101282-35224624	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv541003	chr11:35122694-35261451	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3693078	chr11:35179651-35217745	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35187800-35200800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:35189400-35213800	Weak transcription	Right Ventricle	heart
3	chr11:35189400-35218800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:35189600-35204800	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:35190200-35200000	Weak transcription	Brain Anterior Caudate	brain
6	chr11:35190200-35204400	Weak transcription	Brain Substantia Nigra	brain
7	chr11:35190600-35200400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:35192200-35202000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:35195000-35201200	Weak transcription	Right Atrium	heart
10	chr11:35195000-35211200	Weak transcription	Gastric	stomach
11	chr11:35195800-35201800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:35195800-35213600	Weak transcription	Liver	Liver
13	chr11:35196000-35212200	Weak transcription	Fetal Intestine Small	intestine
14	chr11:35196400-35201600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:35196800-35200400	Weak transcription	Small Intestine	intestine
16	chr11:35196800-35200600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:35196800-35201400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:35197000-35201800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:35197000-35211600	Weak transcription	HUVEC	blood vessel
20	chr11:35197600-35202600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:35197800-35201400	Genic enhancers	Fetal Thymus	thymus
22	chr11:35198000-35200000	Strong transcription	HSMM	muscle
23	chr11:35198000-35200400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:35198000-35200400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:35198000-35200600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:35198000-35201400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:35198000-35202600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:35198000-35202600	Strong transcription	Fetal Stomach	stomach
29	chr11:35198000-35202800	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr11:35198000-35202800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:35198000-35203200	Genic enhancers	Osteobl	bone
32	chr11:35198000-35204400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:35198000-35204400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr11:35198000-35208400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:35198000-35208600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr11:35198000-35223600	Strong transcription	Dnd41	blood
37	chr11:35198000-35232800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:35198200-35200000	Strong transcription	GM12878-XiMat	blood
39	chr11:35198200-35201200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
40	chr11:35198200-35201200	Strong transcription	Left Ventricle	heart
41	chr11:35198200-35202000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
42	chr11:35198200-35202000	Strong transcription	Spleen	Spleen
43	chr11:35198200-35202600	Genic enhancers	HMEC	breast
44	chr11:35198200-35203000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:35198200-35203000	Genic enhancers	NH-A	brain
46	chr11:35198200-35204600	Genic enhancers	NHLF	lung
47	chr11:35198200-35210000	Genic enhancers	NHDF-Ad	bronchial
48	chr11:35198200-35219800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr11:35198400-35200400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:35198400-35200600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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