Variant report

Variant	rs475642
Chromosome Location	chr11:64424691-64424692
allele	A/C
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	chr11:64421262-64425000	U87	brain:	n/a	n/a
2	POLR2A	chr11:64421300-64425022	U87	brain:	n/a	n/a
3	POLR2A	chr11:64411167-64429413	U87	brain:	n/a	n/a
4	CTCF	chr11:64424600-64424750	HCM	heart:	n/a	n/a
5	POLR2A	chr11:64414444-64429407	U87	brain:	n/a	n/a
6	CTCF	chr11:64424133-64424756	K562	blood:	n/a	chr11:64424529-64424542 chr11:64424441-64424448 chr11:64424321-64424334

No.	Distal block	Cell Line	Cell type
1	chr11:64423611..64425758-chr11:64437675..64439983,2	K562	blood:
2	chr11:64418565..64420140-chr11:64423624..64426189,2	K562	blood:
3	chr11:64216755..64217704-chr11:64424374..64424946,2	K562	blood:

Variant related genes	Relation type
NRXN2	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10792441	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897518	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11231825	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11231845	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11602903	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11606370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11607663	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12362590	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12365089	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12786214	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12802649	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1529909	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2021860	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2277311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2360872	0.92[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2360873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2666559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2666563	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35195142	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825016	0.95[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3825018	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs477138	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs492175	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs495130	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs500531	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs504915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs505802	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs506338	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518053	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs524023	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs526338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs528211	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs531763	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs537246	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs538737	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs544838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549461	0.87[ASN][1000 genomes]
rs552307	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs555456	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559946	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs561193	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7102344	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7932437	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs80841	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs893006	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs893007	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9734313	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs475642	DDB1	cis	parietal	SCAN
rs475642	TBC1D10C	cis	cerebellum	SCAN
rs475642	MALAT1	cis	parietal	SCAN
rs475642	TMEM138	cis	cerebellum	SCAN
rs475642	CDC42BPG	cis	parietal	SCAN
rs475642	NRXN2	cis	lung	GTEx
rs475642	EHD1	cis	cerebellum	SCAN
rs475642	POLA2	cis	cerebellum	SCAN

Chromatin state (count:63 , 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	chr11:64420400-64424800	Enhancers	Adipose Nuclei	Adipose
7	chr11:64420400-64425000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:64420400-64425200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr11:64420400-64427800	Enhancers	Fetal Thymus	thymus
10	chr11:64420600-64426600	Weak transcription	A549	lung
11	chr11:64420800-64426400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:64421000-64424800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:64421000-64425000	Weak transcription	Fetal Brain Female	brain
14	chr11:64421000-64425200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:64421000-64427200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:64421000-64434800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:64421200-64427000	Weak transcription	Brain Angular Gyrus	brain
18	chr11:64421200-64453800	Weak transcription	Fetal Brain Male	brain
19	chr11:64421400-64428600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr11:64421800-64424800	Enhancers	Placenta	Placenta
21	chr11:64422000-64425000	Enhancers	Liver	Liver
22	chr11:64422400-64427200	Weak transcription	Brain Substantia Nigra	brain
23	chr11:64422600-64424800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:64422800-64427400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr11:64423000-64430400	Strong transcription	Brain Germinal Matrix	brain
26	chr11:64423000-64432800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:64423400-64425000	Enhancers	HSMMtube	muscle
28	chr11:64423400-64425200	Enhancers	HSMM	muscle
29	chr11:64423600-64425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:64423600-64425200	Enhancers	NHDF-Ad	bronchial
31	chr11:64423600-64427200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:64423800-64424800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr11:64423800-64426000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:64423800-64426400	Enhancers	K562	blood
35	chr11:64424000-64424800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr11:64424000-64425400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:64424000-64426200	Enhancers	Thymus	Thymus
38	chr11:64424000-64427200	Weak transcription	Brain Anterior Caudate	brain
39	chr11:64424200-64424800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr11:64424200-64426000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:64424200-64426000	Enhancers	Fetal Muscle Trunk	muscle
42	chr11:64424200-64426400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr11:64424200-64428400	Weak transcription	Fetal Lung	lung
44	chr11:64424400-64424800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:64424400-64424800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr11:64424400-64425800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:64424400-64426000	Genic enhancers	Osteobl	bone
48	chr11:64424400-64426400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:64424400-64426600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:64424400-64426600	Weak transcription	NHLF	lung

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