Variant report

Variant	rs11901698
Chromosome Location	chr2:53939045-53939046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53938900..53941731-chr2:54013134..54015288,2	K562	blood:
2	chr2:53931144..53933214-chr2:53937294..53940246,2	K562	blood:

Variant related genes	Relation type
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10490468	0.92[CHB][hapmap];0.91[YRI][hapmap]
rs11897282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1232	0.84[CHB][hapmap]
rs13408029	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17045176	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs17045203	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs17520505	0.93[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17521008	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2008082	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287340	1.00[CHB][hapmap]
rs2302797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2542572	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2542578	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2542580	0.86[EUR][1000 genomes]
rs2542581	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2542582	0.92[CHB][hapmap]
rs2542589	0.93[CHB][hapmap]
rs2542591	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs2542592	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2543629	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs2692519	0.92[CHB][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap]
rs2692523	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2692533	0.92[CHB][hapmap];0.80[JPT][hapmap];0.84[YRI][hapmap]
rs2692535	0.81[AFR][1000 genomes]
rs2949813	0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs35772199	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3731970	0.84[YRI][hapmap]
rs3770394	1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3770395	0.82[ASN][1000 genomes]
rs3770399	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770407	0.91[YRI][hapmap]
rs3770411	0.84[CEU][hapmap];0.92[CHB][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs4116709	0.93[CHB][hapmap];0.91[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56214822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56228834	0.87[ASN][1000 genomes]
rs62137565	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62137566	0.81[AMR][1000 genomes]
rs62137573	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62137602	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62137606	0.82[ASN][1000 genomes]
rs6730006	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs719127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72901256	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7558968	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7583622	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs7600817	0.82[ASN][1000 genomes]
rs805316	0.84[CHB][hapmap]
rs805435	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs805437	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1011449	chr2:53894529-53947781	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1009107	chr2:53896767-53946913	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014949	chr2:53896767-53947781	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1011400	chr2:53899956-53947781	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv1844655	chr2:53929855-53972693	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
3	chr2:53910000-53941600	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
7	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
8	chr2:53927600-53960200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:53933800-53944000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:53934200-53942200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:53934800-53939200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:53935400-53939200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:53936600-53939800	Weak transcription	Osteobl	bone
14	chr2:53936600-53940000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:53936600-53940200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:53936600-53941000	Strong transcription	Fetal Stomach	stomach
17	chr2:53936600-53941400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:53936600-53941800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:53936600-53941800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr2:53936600-53944200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:53936600-53945400	Weak transcription	Colonic Mucosa	Colon
22	chr2:53936600-53968400	Weak transcription	Pancreas	Pancrea
23	chr2:53936600-53978600	Weak transcription	Hela-S3	cervix
24	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:53937000-53940400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:53937000-53943400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:53937000-53944200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr2:53937000-53983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:53937200-53940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:53937200-53941200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:53937200-53941200	Weak transcription	Brain Angular Gyrus	brain
33	chr2:53937200-53941200	Weak transcription	Brain Anterior Caudate	brain
34	chr2:53937200-53943200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:53937200-53944000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:53937200-53944800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:53937200-53949400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:53937200-53954000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:53937200-53955800	Weak transcription	Brain Substantia Nigra	brain
40	chr2:53937200-53961400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:53937200-53964400	Weak transcription	Aorta	Aorta
42	chr2:53937200-53966800	Weak transcription	Gastric	stomach
43	chr2:53937200-53978600	Weak transcription	NH-A	brain
44	chr2:53937200-53983600	Weak transcription	Right Ventricle	heart
45	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:53937400-53940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:53937400-53941200	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:53937400-53941800	Strong transcription	Primary T cells from cord blood	blood
49	chr2:53937400-53943200	Weak transcription	Ovary	ovary
50	chr2:53937400-53944000	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links