Variant report

Variant	rs11688829
Chromosome Location	chr2:98528689-98528690
allele	A/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	BATF	chr2:98528619-98528931	GM12878	blood:	n/a	n/a
2	EP300	chr2:98528662-98528969	GM12878	blood:	n/a	n/a
3	SPI1	chr2:98528607-98528856	GM12891	blood:	n/a	n/a
4	BATF	chr2:98528641-98528974	GM12878	blood:	n/a	n/a
5	ZNF384	chr2:98527804-98528708	GM12878	blood:	n/a	n/a
6	CUX1	chr2:98528414-98529007	GM12878	blood:	n/a	n/a
7	KAP1	chr2:98527771-98528697	K562	blood:	n/a	n/a
8	NFIC	chr2:98527724-98529054	GM12878	blood:	n/a	n/a
9	ARID3A	chr2:98527005-98528708	K562	blood:	n/a	n/a
10	BCL11A	chr2:98528607-98528978	GM12878	blood:	n/a	n/a
11	EBF1	chr2:98527719-98529193	GM12878	blood:	n/a	n/a
12	GATA3	chr2:98527734-98529092	SK-N-SH	brain:	n/a	chr2:98528890-98528899 chr2:98528105-98528114 chr2:98528892-98528899 chr2:98528888-98528901 chr2:98528890-98528900 chr2:98528100-98528121
13	ZMIZ1	chr2:98527587-98528836	K562	blood:	n/a	n/a
14	SPI1	chr2:98528563-98528799	GM12878	blood:	n/a	n/a
15	CEBPB	chr2:98527925-98528945	Hela-S3	cervix:	n/a	n/a
16	EBF1	chr2:98528606-98529005	GM12878	blood:	n/a	n/a
17	RELA	chr2:98528653-98529307	GM12891	blood:	n/a	n/a
18	SMARCA4	chr2:98527342-98528932	K562	blood:	n/a	n/a
19	BHLHE40	chr2:98528627-98528946	GM12878	blood:	n/a	n/a
20	EBF1	chr2:98528594-98528965	GM12878	blood:	n/a	n/a
21	EP300	chr2:98528626-98529172	GM12878	blood:	n/a	n/a
22	RUNX3	chr2:98528504-98529062	GM12878	blood:	n/a	n/a
23	RELA	chr2:98528618-98529164	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98525286..98526866-chr2:98527040..98529570,2	MCF-7	breast:
2	chr2:98522726..98524579-chr2:98527154..98529233,2	K562	blood:

Variant related genes	Relation type
TMEM131	TF binding region
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10432626	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11678558	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs11678591	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11679828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680018	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680321	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11680883	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11681535	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11684749	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11686881	0.91[CEU][hapmap]
rs11687510	0.87[CEU][hapmap]
rs11690687	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11690737	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11691494	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11692010	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11692470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052222	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12052836	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12052846	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12104810	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12988571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12995673	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13004090	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13006932	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13008968	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13020776	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13023980	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13028954	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13032265	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13032883	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13033383	0.91[CEU][hapmap]
rs13034929	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1470483	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17488834	0.92[CEU][hapmap]
rs17488897	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17489287	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs17489454	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17489915	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17489984	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17490429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838797	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1875699	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2044458	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2044459	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084176	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278700	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2305143	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2871183	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3192177	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs3198055	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34149969	0.82[EUR][1000 genomes]
rs34373359	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34502870	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34503448	0.86[EUR][1000 genomes]
rs34528940	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34654057	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34974566	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35098301	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35218942	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255677	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35424768	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35505530	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35564270	0.85[EUR][1000 genomes]
rs35783535	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4311104	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55776387	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55861914	0.82[AFR][1000 genomes]
rs55886305	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57836517	0.83[AFR][1000 genomes]
rs58546246	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62156511	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710088	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6711101	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6738389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6746768	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6748124	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6757357	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71412824	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71429376	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs717417	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7421146	0.91[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7564773	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7583868	0.85[EUR][1000 genomes]
rs7601898	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs895438	1.00[CEU][hapmap];0.92[GIH][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs953320	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

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	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking 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	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98503800-98536400	Weak transcription	HSMMtube	muscle
2	chr2:98504000-98533800	Weak transcription	Spleen	Spleen
3	chr2:98504000-98538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:98504000-98540600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:98504000-98540800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:98504200-98530800	Weak transcription	Thymus	Thymus
7	chr2:98504600-98540800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:98504600-98552200	Weak transcription	NHLF	lung
9	chr2:98505400-98528800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:98505400-98530200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:98507600-98535000	Weak transcription	Brain Anterior Caudate	brain
12	chr2:98509000-98536400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:98515800-98540800	Weak transcription	Aorta	Aorta
14	chr2:98516400-98534600	Weak transcription	A549	lung
15	chr2:98519600-98541600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:98519800-98538600	Weak transcription	Gastric	stomach
17	chr2:98520200-98546000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:98520200-98552200	Weak transcription	Brain Angular Gyrus	brain
19	chr2:98520600-98550600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:98520800-98540400	Weak transcription	Lung	lung
21	chr2:98521200-98532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:98521800-98540400	Weak transcription	Colonic Mucosa	Colon
23	chr2:98523200-98536200	Weak transcription	Ovary	ovary
24	chr2:98523200-98540600	Weak transcription	Right Ventricle	heart
25	chr2:98523400-98528800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:98523400-98530200	Weak transcription	Fetal Thymus	thymus
27	chr2:98523400-98530200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:98523400-98536000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:98523400-98536400	Weak transcription	Esophagus	oesophagus
30	chr2:98523400-98536600	Weak transcription	HSMM	muscle
31	chr2:98523400-98540600	Weak transcription	Fetal Brain Female	brain
32	chr2:98523400-98545800	Weak transcription	Fetal Kidney	kidney
33	chr2:98523400-98546200	Weak transcription	HUVEC	blood vessel
34	chr2:98523600-98530800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:98523800-98537600	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:98524400-98532600	Weak transcription	HMEC	breast
37	chr2:98524600-98552600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:98524800-98529000	Weak transcription	Fetal Stomach	stomach
39	chr2:98524800-98530400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:98524800-98532400	Enhancers	Primary B cells from peripheral blood	blood
41	chr2:98524800-98532400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:98524800-98540800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:98524800-98552200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:98525000-98528800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:98525000-98529000	Weak transcription	Right Atrium	heart
46	chr2:98525000-98530600	Weak transcription	Dnd41	blood
47	chr2:98525000-98532400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:98525000-98534000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:98525000-98536000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:98525000-98536200	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links