Variant report

Variant	rs11900461
Chromosome Location	chr2:97615993-97615994
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	SMC3	chr2:97615968-97617531	SK-N-SH	brain:	n/a	chr2:97617084-97617098 chr2:97616504-97616512 chr2:97616817-97616831 chr2:97617064-97617071
2	RAD21	chr2:97615932-97617540	SK-N-SH	brain:	n/a	chr2:97617080-97617099 chr2:97617089-97617098 chr2:97617084-97617098 chr2:97616796-97616805 chr2:97617229-97617241

No.	Distal block	Cell Line	Cell type
1	chr2:97533737..97536220-chr2:97612669..97617368,4	K562	blood:
2	chr2:97481193..97483827-chr2:97615548..97618256,2	MCF-7	breast:
3	chr2:97557540..97561219-chr2:97615825..97618671,3	MCF-7	breast:
4	chr2:97530625..97533961-chr2:97614118..97617148,3	K562	blood:
5	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
6	chr2:97562462..97564886-chr2:97613357..97616382,3	MCF-7	breast:
7	chr2:97521500..97526453-chr2:97614513..97620136,8	K562	blood:
8	chr2:97521500..97526547-chr2:97614513..97619168,8	K562	blood:
9	chr2:97534744..97537184-chr2:97615647..97618608,4	K562	blood:

Variant related genes	Relation type
FAM178B	TF binding region
ENSG00000163126	Chromatin interaction
ENSG00000168754	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000213337	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11890407	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57035274	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59178801	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60019075	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60608738	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6728642	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73959416	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7580504	0.89[EUR][1000 genomes]
rs7584641	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7593754	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription 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	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' 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	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97606200-97616000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:97610400-97616600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:97610400-97617400	Enhancers	Brain Substantia Nigra	brain
4	chr2:97611000-97616400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:97611000-97616600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:97611200-97616000	Weak transcription	Fetal Thymus	thymus
7	chr2:97611200-97616200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:97611200-97616400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:97611200-97616400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:97611200-97616800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:97611200-97618000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:97611400-97616000	Weak transcription	Fetal Brain Female	brain
13	chr2:97611400-97616000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:97611600-97616000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:97612800-97620200	Enhancers	K562	blood
16	chr2:97613200-97616600	Enhancers	Brain Angular Gyrus	brain
17	chr2:97613200-97617400	Enhancers	Brain Anterior Caudate	brain
18	chr2:97614200-97616600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:97614600-97616600	Weak transcription	Esophagus	oesophagus
20	chr2:97614800-97619800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr2:97615200-97618200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:97615400-97616000	Enhancers	Colon Smooth Muscle	Colon
23	chr2:97615400-97617200	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr2:97615400-97617400	Bivalent Enhancer	Fetal Stomach	stomach
25	chr2:97615400-97621800	Enhancers	Colonic Mucosa	Colon
26	chr2:97615600-97616000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr2:97615600-97616000	Bivalent Enhancer	HepG2	liver
28	chr2:97615600-97616600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:97615600-97617000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:97615600-97617200	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr2:97615600-97617200	Bivalent Enhancer	Placenta	Placenta
32	chr2:97615600-97617400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:97615600-97617600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:97615600-97620800	Enhancers	Fetal Brain Male	brain
35	chr2:97615600-97620800	Enhancers	Ovary	ovary
36	chr2:97615800-97616000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:97615800-97616000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr2:97615800-97616200	Enhancers	Stomach Smooth Muscle	stomach
39	chr2:97615800-97616600	Enhancers	Primary T cells fromperipheralblood	blood
40	chr2:97615800-97617200	Enhancers	Spleen	Spleen
41	chr2:97615800-97617400	Enhancers	Fetal Heart	heart
42	chr2:97615800-97617600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr2:97615800-97619000	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr2:97615800-97620800	Enhancers	Fetal Lung	lung

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