Variant report

Variant	rs7939965
Chromosome Location	chr11:64425024-64425025
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	chr11:64411167-64429413	U87	brain:	n/a	n/a
2	GATA2	chr11:64424832-64425224	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr11:64414444-64429407	U87	brain:	n/a	n/a
4	GATA3	chr11:64424949-64425149	MCF-7	breast:	n/a	n/a
5	GATA3	chr11:64424926-64425262	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64424901..64427450-chr11:64452381..64454020,2	K562	blood:
2	chr11:64423611..64425758-chr11:64437675..64439983,2	K562	blood:
3	chr11:64418565..64420140-chr11:64423624..64426189,2	K562	blood:

Variant related genes	Relation type
NRXN2	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10400348	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10792444	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897524	0.81[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10897525	0.88[MEX][hapmap]
rs11231853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231859	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs11231869	0.88[MEX][hapmap]
rs1143937	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs1207181	0.83[EUR][1000 genomes]
rs12417551	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12575704	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633462	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17146121	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2003293	0.89[EUR][1000 genomes]
rs2073798	0.93[GIH][hapmap];0.89[MEX][hapmap]
rs2230414	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2267918	0.89[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2284301	0.89[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2375335	0.87[EUR][1000 genomes]
rs2959652	0.89[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs3741398	0.89[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs3809076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474707	0.89[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs475688	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs476037	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs477549	0.89[CEU][hapmap];0.89[MEX][hapmap];0.84[EUR][1000 genomes]
rs483962	0.89[CEU][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs487105	0.89[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs489192	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs490980	0.81[EUR][1000 genomes]
rs494128	0.86[EUR][1000 genomes]
rs496914	0.89[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs523200	0.89[CEU][hapmap];0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs532747	0.82[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs547066	0.92[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs569602	0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs580374	0.87[EUR][1000 genomes]
rs58483071	0.89[EUR][1000 genomes]
rs589691	0.89[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.86[EUR][1000 genomes]
rs593394	0.84[EUR][1000 genomes]
rs606458	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs607389	0.89[CEU][hapmap]
rs620006	0.86[EUR][1000 genomes]
rs624975	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs625172	0.93[GIH][hapmap];0.89[MEX][hapmap]
rs633923	0.82[EUR][1000 genomes]
rs637332	0.89[CEU][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs667237	0.82[EUR][1000 genomes]
rs669976	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs674297	0.82[EUR][1000 genomes]
rs677298	0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs680273	0.89[CEU][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes]
rs693235	0.80[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs72643567	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72643568	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS 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	1075 gene(s)	inside rSNPs	diseases
9	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
10	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS 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	1075 gene(s)	inside rSNPs	diseases
11	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
13	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7939965	PYGM	cis	cerebellum	SCAN
rs7939965	TMEM138	cis	parietal	SCAN
rs7939965	B3GNT1	cis	cerebellum	SCAN
rs7939965	CABP2	cis	parietal	SCAN
rs7939965	RAB3IL1	cis	parietal	SCAN
rs7939965	EHD1	cis	cerebellum	SCAN
rs7939965	ANKRD13D	cis	parietal	SCAN
rs7939965	TMEM138	cis	cerebellum	SCAN
rs7939965	SF1	cis	lymphoblastoid	seeQTL
rs7939965	LRRN4CL	cis	cerebellum	SCAN
rs7939965	PYGM	cis	parietal	SCAN
rs7939965	MALAT1	cis	parietal	SCAN
rs7939965	SF1	cis	multi-tissue	Pritchard
rs7939965	POLA2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64411600-64427800	Weak transcription	Aorta	Aorta
2	chr11:64412400-64428200	Weak transcription	Right Atrium	heart
3	chr11:64412600-64425600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:64415800-64430000	Weak transcription	Gastric	stomach
5	chr11:64420200-64426200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:64420400-64425200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr11:64420400-64427800	Enhancers	Fetal Thymus	thymus
8	chr11:64420600-64426600	Weak transcription	A549	lung
9	chr11:64420800-64426400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:64421000-64425200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:64421000-64427200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:64421000-64434800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:64421200-64427000	Weak transcription	Brain Angular Gyrus	brain
14	chr11:64421200-64453800	Weak transcription	Fetal Brain Male	brain
15	chr11:64421400-64428600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:64422400-64427200	Weak transcription	Brain Substantia Nigra	brain
17	chr11:64422800-64427400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr11:64423000-64430400	Strong transcription	Brain Germinal Matrix	brain
19	chr11:64423000-64432800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:64423400-64425200	Enhancers	HSMM	muscle
21	chr11:64423600-64425200	Enhancers	NHDF-Ad	bronchial
22	chr11:64423600-64427200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:64423800-64426000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:64423800-64426400	Enhancers	K562	blood
25	chr11:64424000-64425400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:64424000-64426200	Enhancers	Thymus	Thymus
27	chr11:64424000-64427200	Weak transcription	Brain Anterior Caudate	brain
28	chr11:64424200-64426000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:64424200-64426000	Enhancers	Fetal Muscle Trunk	muscle
30	chr11:64424200-64426400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:64424200-64428400	Weak transcription	Fetal Lung	lung
32	chr11:64424400-64425800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:64424400-64426000	Genic enhancers	Osteobl	bone
34	chr11:64424400-64426400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:64424400-64426600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:64424400-64426600	Weak transcription	NHLF	lung
37	chr11:64424400-64427200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr11:64424400-64427400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:64424400-64435200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr11:64424600-64425800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:64424600-64426600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:64424600-64426600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr11:64424600-64426600	Weak transcription	Fetal Muscle Leg	muscle
44	chr11:64424600-64426600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:64424600-64426600	Weak transcription	Spleen	Spleen
46	chr11:64424600-64426800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr11:64424600-64426800	Enhancers	Hela-S3	cervix
48	chr11:64424600-64427200	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:64424600-64427800	Weak transcription	Fetal Stomach	stomach
50	chr11:64424800-64425800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links