Variant report

Variant	rs11676758
Chromosome Location	chr2:114484300-114484301
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	POLR2A	chr2:114484281-114484350	A549	lung:	n/a	n/a
2	POLR2A	chr2:114484118-114484540	K562	blood:	n/a	n/a
3	POLR2A	chr2:114484261-114484691	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:114484206-114484432	K562	blood:	n/a	n/a
5	POLR2A	chr2:114484223-114484372	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:114484097-114484474	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:114484161-114484476	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114476035..114479420-chr2:114481411..114484659,3	K562	blood:
2	chr2:114482332..114485532-chr2:114485677..114488517,3	K562	blood:

Variant related genes	Relation type
SLC35F5	TF binding region
ENSG00000265429	Chromatin interaction
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674510	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11677881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11678202	0.81[CHB][hapmap]
rs11679736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11685171	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11687572	0.97[ASN][1000 genomes]
rs11694541	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17632073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633527	0.93[ASN][1000 genomes]
rs17683666	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17684620	0.92[ASN][1000 genomes]
rs2166965	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41377545	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4849271	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58351064	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6708711	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6709158	0.81[CHB][hapmap]
rs6725990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726001	0.81[CHB][hapmap]
rs6732182	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73955055	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955056	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955057	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955059	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73955070	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7581858	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7599741	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7599832	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9753198	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11676758	DDX11L2	cis	Esophagus Mucosa	GTEx
rs11676758	DDX11L2	cis	Nerve Tibial	GTEx
rs11676758	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs11676758	DDX11L2	cis	Whole Blood	GTEx
rs11676758	RPL23AP7	cis	Whole Blood	GTEx
rs11676758	DDX11L2	cis	Adipose Subcutaneous	GTEx
rs11676758	RPL23AP7	cis	Artery Tibial	GTEx
rs11676758	RPL23AP7	cis	Heart Left Ventricle	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114486200	Weak transcription	Dnd41	blood
2	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
6	chr2:114461600-114484400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:114461600-114499800	Weak transcription	Hela-S3	cervix
8	chr2:114462000-114497400	Weak transcription	Colonic Mucosa	Colon
9	chr2:114463000-114498800	Weak transcription	Esophagus	oesophagus
10	chr2:114464000-114497600	Weak transcription	Right Ventricle	heart
11	chr2:114464000-114497600	Weak transcription	Spleen	Spleen
12	chr2:114464600-114484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:114465200-114486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
15	chr2:114465800-114484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:114467400-114497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:114467600-114486200	Weak transcription	Fetal Brain Male	brain
18	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:114469400-114510400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:114469800-114486400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:114470000-114497400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:114470000-114500200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:114470200-114493400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:114470200-114511200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr2:114470400-114510800	Strong transcription	HSMM	muscle
26	chr2:114471000-114486000	Weak transcription	K562	blood
27	chr2:114471000-114488200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:114471000-114495600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:114471000-114495600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:114471000-114498600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:114471000-114500200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:114472800-114486200	Weak transcription	A549	lung
33	chr2:114472800-114486600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:114473200-114488600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:114473200-114494600	Weak transcription	Fetal Heart	heart
36	chr2:114473400-114484800	Weak transcription	HMEC	breast
37	chr2:114473800-114497200	Weak transcription	NHEK	skin
38	chr2:114474400-114486000	Weak transcription	GM12878-XiMat	blood
39	chr2:114474400-114494600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:114474400-114507600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:114475200-114486400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:114475600-114486200	Weak transcription	Brain Substantia Nigra	brain
43	chr2:114475600-114486800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:114476000-114506600	Weak transcription	Thymus	Thymus
45	chr2:114476800-114484600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:114477000-114484600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:114477200-114488200	Weak transcription	NH-A	brain
48	chr2:114478800-114486400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:114478800-114487200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr2:114478800-114504400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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