Variant report

Variant	rs11889101
Chromosome Location	chr2:97590888-97590889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97587758..97596829-chr2:97597446..97601811,11	K562	blood:
2	chr2:97522694..97525971-chr2:97587998..97591660,3	K562	blood:
3	chr2:97583057..97585198-chr2:97588467..97591915,3	K562	blood:
4	chr2:97548252..97550212-chr2:97588588..97591450,2	MCF-7	breast:
5	chr2:97570898..97573698-chr2:97588276..97590943,2	K562	blood:
6	chr2:97589310..97591841-chr2:97591978..97596020,4	MCF-7	breast:
7	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
8	chr2:97588776..97591371-chr2:97597850..97600657,3	MCF-7	breast:
9	chr2:97556750..97558871-chr2:97588696..97591655,2	MCF-7	breast:
10	chr2:97556985..97558977-chr2:97588786..97591585,2	K562	blood:
11	chr2:97584997..97587138-chr2:97589413..97591489,2	MCF-7	breast:
12	chr2:97590809..97593385-chr2:97597939..97599860,2	MCF-7	breast:
13	chr2:97590638..97593151-chr2:97603890..97606956,4	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNNM3-1	chr2:97589781-97591573	ENSG00000246515
2	lnc-CNNM3-1	chr2:97589781-97591574	NONHSAT072593

No data

Variant related genes	Relation type
ENSG00000163126	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000213337	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11900466	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119655	0.97[ASN][1000 genomes]
rs3903548	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57397886	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58232717	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59660613	0.97[ASN][1000 genomes]
rs60063645	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62152900	0.89[ASN][1000 genomes]
rs62152908	0.97[ASN][1000 genomes]
rs62152910	0.97[ASN][1000 genomes]
rs6708171	0.89[ASN][1000 genomes]
rs6717064	0.97[ASN][1000 genomes]
rs6734326	0.92[ASN][1000 genomes]
rs6734673	0.97[ASN][1000 genomes]
rs6746020	0.92[ASN][1000 genomes]
rs72811653	0.97[ASN][1000 genomes]
rs72811663	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811667	1.00[ASN][1000 genomes]
rs7591775	1.00[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	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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97582600-97593000	Weak transcription	Right Atrium	heart
2	chr2:97585200-97591000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:97587000-97592200	Weak transcription	Brain Germinal Matrix	brain
4	chr2:97589400-97591000	Enhancers	Primary hematopoietic stem cells	blood
5	chr2:97589400-97593800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:97589600-97591200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr2:97589600-97591200	Enhancers	Fetal Heart	heart
8	chr2:97589600-97591400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr2:97589600-97591600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr2:97589600-97593200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:97589800-97591000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:97589800-97591000	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr2:97589800-97591000	Flanking Active TSS	Brain Substantia Nigra	brain
14	chr2:97589800-97591000	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr2:97589800-97591200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr2:97589800-97591200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr2:97589800-97591200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr2:97589800-97591200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr2:97589800-97591400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:97589800-97595200	Enhancers	Fetal Brain Male	brain
21	chr2:97590000-97591000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:97590000-97591600	Enhancers	K562	blood
23	chr2:97590000-97592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:97590200-97591000	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr2:97590200-97591400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:97590400-97591000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:97590400-97591000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr2:97590400-97591000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:97590400-97592800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:97590400-97593200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:97590600-97591000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr2:97590600-97591000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:97590600-97591200	Enhancers	Fetal Stomach	stomach
34	chr2:97590600-97591200	Enhancers	Rectal Smooth Muscle	rectum
35	chr2:97590600-97591600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:97590600-97592200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:97590600-97592200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:97590600-97593600	Enhancers	Brain Angular Gyrus	brain
39	chr2:97590800-97591000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:97590800-97591000	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr2:97590800-97591000	Enhancers	Fetal Brain Female	brain
42	chr2:97590800-97591200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:97590800-97591200	Enhancers	Fetal Thymus	thymus
44	chr2:97590800-97592800	Enhancers	Colon Smooth Muscle	Colon
45	chr2:97590800-97592800	Weak transcription	Spleen	Spleen
46	chr2:97590800-97593200	Weak transcription	Fetal Lung	lung

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