Variant report

Variant	rs6762432
Chromosome Location	chr3:150123996-150123997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150122822..150130151-chr3:150261910..150267967,8	K562	blood:
2	chr3:150111194..150113689-chr3:150123124..150124651,2	MCF-7	breast:
3	chr3:150116751..150119532-chr3:150121582..150125856,6	K562	blood:
4	chr3:150121790..150130149-chr3:150138506..150143439,10	MCF-7	breast:
5	chr19:55917718..55920668-chr3:150122792..150125732,2	K562	blood:
6	chr3:150105305..150107998-chr3:150123098..150125972,3	K562	blood:
7	chr3:150101805..150104730-chr3:150121434..150125041,3	K562	blood:
8	chr3:149953873..149961412-chr3:150123750..150131229,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108106	Chromatin interaction
ENSG00000244541	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000144895	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10513374	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10935800	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11711035	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11719977	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12638309	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12639090	0.91[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs13081231	0.82[ASN][1000 genomes]
rs13082720	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13099758	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13321876	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1450335	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1450336	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1450344	0.83[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs16862651	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1868672	0.83[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1868673	0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2167177	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28514580	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2868425	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4423794	0.91[JPT][hapmap]
rs4681203	0.82[ASN][1000 genomes]
rs4681205	0.82[JPT][hapmap]
rs4681206	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4681615	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681618	0.88[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4681619	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs58628422	0.82[ASN][1000 genomes]
rs67319423	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6770424	0.83[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6784048	0.82[ASN][1000 genomes]
rs6792734	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792759	0.83[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6795124	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6810143	0.83[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs7427177	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626725	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7651353	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7651989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9784281	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9784335	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9813752	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9826729	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9846873	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9865031	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9882777	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][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	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1818335	chr3:150122121-150128717	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6762432	TSC22D2	cis	cerebellum	SCAN
rs6762432	AADACL2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150090200-150124600	Weak transcription	Aorta	Aorta
2	chr3:150109200-150124400	Weak transcription	HSMM	muscle
3	chr3:150109200-150124600	Weak transcription	NHLF	lung
4	chr3:150117000-150125000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:150117200-150125000	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:150117400-150125000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:150119600-150124600	Weak transcription	Fetal Intestine Large	intestine
8	chr3:150119600-150124600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:150120200-150124800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:150121400-150124800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:150121600-150125200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:150121800-150124800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:150121800-150124800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:150121800-150124800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:150121800-150125000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:150122200-150124200	Weak transcription	HSMMtube	muscle
17	chr3:150122200-150124400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:150122200-150124800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:150122200-150124800	Weak transcription	Hela-S3	cervix
20	chr3:150122200-150125000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:150122200-150125200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:150122400-150124400	Weak transcription	NHEK	skin
23	chr3:150122400-150124600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:150122400-150124600	Weak transcription	HMEC	breast
25	chr3:150122400-150124600	Weak transcription	NHDF-Ad	bronchial
26	chr3:150123400-150124200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:150123600-150124400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:150123600-150124600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:150123600-150125200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr3:150123800-150124400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:150123800-150124600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:150123800-150124600	Weak transcription	A549	lung
33	chr3:150123800-150124600	Enhancers	HUVEC	blood vessel
34	chr3:150123800-150125000	Weak transcription	Small Intestine	intestine

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