Variant report

Variant	rs2403227
Chromosome Location	chr11:9984138-9984139
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	ATF2	chr11:9984115-9984704	GM12878	blood:	n/a	n/a
2	NFIC	chr11:9984135-9984738	GM12878	blood:	n/a	n/a
3	SPI1	chr11:9983953-9984735	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000254765	TF binding region

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10500715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10500717	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10743123	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10770077	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10770078	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770079	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs10840327	0.86[CEU][hapmap]
rs10840330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840337	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs10840338	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs10840347	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10840348	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10840359	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10840361	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10840362	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10840370	0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs11042543	0.81[CEU][hapmap]
rs11042558	0.89[ASN][1000 genomes]
rs11042559	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11042561	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs11042571	0.91[EUR][1000 genomes]
rs11042573	0.84[EUR][1000 genomes]
rs11042574	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11042578	0.90[EUR][1000 genomes]
rs11042579	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11042580	0.88[EUR][1000 genomes]
rs11042589	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11042590	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11042591	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs11042595	0.86[CEU][hapmap]
rs11042601	0.86[CEU][hapmap]
rs11042604	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11042605	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11042609	0.86[CEU][hapmap]
rs11042613	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs11042615	0.86[CEU][hapmap]
rs11042618	0.86[CEU][hapmap]
rs11042623	0.84[CEU][hapmap]
rs11042624	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs11042632	0.89[CEU][hapmap]
rs11042639	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs11042641	0.81[CEU][hapmap]
rs11042645	1.00[JPT][hapmap]
rs11530489	0.87[YRI][hapmap]
rs11600251	0.86[CEU][hapmap]
rs11602465	0.87[EUR][1000 genomes]
rs11602515	0.87[CEU][hapmap]
rs11603440	0.88[EUR][1000 genomes]
rs11606561	0.86[CEU][hapmap]
rs12222953	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12281072	0.86[YRI][hapmap]
rs12283105	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12290996	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364676	0.80[EUR][1000 genomes]
rs12419923	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs12420734	0.89[CEU][hapmap]
rs12420950	0.85[EUR][1000 genomes]
rs12421096	0.86[CEU][hapmap]
rs12421200	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs12575719	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1372807	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs1442732	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs16907368	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs16907396	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs17271847	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs17356792	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs17359113	0.86[CEU][hapmap]
rs2403226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2403229	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478985	0.81[EUR][1000 genomes]
rs4529876	0.83[EUR][1000 genomes]
rs4576815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625455	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4909915	0.87[CEU][hapmap]
rs4909917	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910080	0.83[CEU][hapmap]
rs4910081	0.86[CEU][hapmap]
rs4910086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58084362	0.91[ASN][1000 genomes]
rs60362241	0.91[ASN][1000 genomes]
rs7106914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7114044	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7114303	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7123453	0.86[CEU][hapmap]
rs7131445	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs7928959	0.86[CEU][hapmap]
rs7933475	0.99[ASN][1000 genomes]
rs7938491	0.86[CEU][hapmap]
rs7938502	0.86[CEU][hapmap]
rs7938647	0.86[CEU][hapmap]
rs7938788	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7946995	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs7950447	0.86[CEU][hapmap]
rs7951950	0.97[ASN][1000 genomes]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv1819684	chr11:9973062-10012511	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9952800-9995200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9968000-9984200	Weak transcription	Fetal Kidney	kidney
3	chr11:9973000-9986000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
5	chr11:9974200-9994400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:9974200-9994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:9974200-9994800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:9974200-9999000	Weak transcription	Fetal Heart	heart
9	chr11:9974200-9999000	Weak transcription	HSMMtube	muscle
10	chr11:9975400-9985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:9977000-9994400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr11:9978600-9986000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:9978800-9985000	Weak transcription	Small Intestine	intestine
14	chr11:9979400-9986000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr11:9979400-9995000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:9979600-9985600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:9979600-9985800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:9979600-9994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr11:9979800-9987400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:9979800-9999200	Weak transcription	NH-A	brain
21	chr11:9980200-9984800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:9980200-9985800	Strong transcription	Liver	Liver
23	chr11:9980200-9985800	Strong transcription	Placenta	Placenta
24	chr11:9980200-9986000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr11:9981000-10020000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:9981200-9984400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr11:9981200-9988400	Weak transcription	HMEC	breast
28	chr11:9981200-9990000	Weak transcription	A549	lung
29	chr11:9981200-9990600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:9981200-9995000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:9981200-10004200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:9981200-10009200	Weak transcription	Brain Germinal Matrix	brain
33	chr11:9981400-9984400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:9981400-9984400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr11:9981400-9984800	Weak transcription	Fetal Intestine Large	intestine
36	chr11:9981400-9985000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:9981400-9985400	Weak transcription	Fetal Intestine Small	intestine
38	chr11:9981400-9985600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:9981400-9986600	Weak transcription	Pancreas	Pancrea
40	chr11:9981400-9987000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:9981400-9989000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:9981400-9989000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:9981400-9989600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr11:9981400-9990600	Weak transcription	Colon Smooth Muscle	Colon
45	chr11:9981400-9990600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr11:9981400-9992200	Weak transcription	Brain Substantia Nigra	brain
47	chr11:9981400-9993400	Weak transcription	Spleen	Spleen
48	chr11:9981400-9994400	Weak transcription	HUVEC	blood vessel
49	chr11:9981400-9994600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr11:9981400-9994600	Weak transcription	NHLF	lung

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