Variant report

Variant	rs751075
Chromosome Location	chr3:51377300-51377301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51376546..51378472-chr3:51379958..51381603,2	MCF-7	breast:
2	chr3:51373593..51375810-chr3:51376800..51379121,2	K562	blood:
3	chr3:51367010..51371078-chr3:51375773..51379297,4	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10212250	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs1031925	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1055429	0.82[AMR][1000 genomes]
rs10865970	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130282	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11130293	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11721253	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12632046	0.84[EUR][1000 genomes]
rs1383251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1383252	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1480353	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1480354	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1480357	0.85[JPT][hapmap];0.91[MEX][hapmap]
rs1480358	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1480363	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1542574	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1552072	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs1552073	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs1552074	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051734	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs17051762	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2061951	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2127655	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2219890	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2241784	0.82[EUR][1000 genomes]
rs2355934	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs2355941	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs4244697	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs4301044	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs4328835	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4367101	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4378999	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4428169	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4453876	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs4528983	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4532165	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs4568177	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs4611808	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687569	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974095	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs4974104	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4974105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974106	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974109	0.85[JPT][hapmap];0.91[MEX][hapmap]
rs6445455	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs6445551	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs6445620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6445622	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];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6445624	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6445628	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];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6772664	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs6773260	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6777719	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs6779658	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs6793900	0.82[AMR][1000 genomes]
rs6809080	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7372658	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7427006	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7619584	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7625006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628533	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs7633708	0.83[CEU][hapmap]
rs7644957	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs7648012	0.91[CEU][hapmap]
rs922612	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs9311469	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9855442	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9858412	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs9869123	1.00[CHB][hapmap]
rs9878100	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs9883739	0.85[CHB][hapmap];0.85[JPT][hapmap]

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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs751075	NCKIPSD	cis	cerebellum	SCAN
rs751075	TEX264	cis	Nerve Tibial	GTEx
rs751075	HEMK1	cis	cerebellum	SCAN
rs751075	TEX264	cis	Artery Tibial	GTEx
rs751075	HYAL2	cis	parietal	SCAN
rs751075	TEX264	cis	Esophagus Muscularis	GTEx
rs751075	MST1	cis	cerebellum	SCAN
rs751075	IQCF2	cis	parietal	SCAN
rs751075	PARP3	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51353400-51377600	Weak transcription	Left Ventricle	heart
2	chr3:51358800-51377400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:51366400-51377600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:51366600-51377400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:51367600-51377800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:51368000-51377400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:51369400-51377400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:51369600-51383800	Weak transcription	Fetal Brain Male	brain
9	chr3:51372200-51377800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:51372400-51377400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:51374800-51377600	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:51375000-51377600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:51375000-51377800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:51375200-51377800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:51375400-51377600	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:51375400-51377600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:51375400-51378000	Strong transcription	Fetal Brain Female	brain
18	chr3:51375600-51377600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:51375600-51379000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:51375800-51377400	Enhancers	NHDF-Ad	bronchial
21	chr3:51375800-51377600	Enhancers	Osteobl	bone
22	chr3:51376000-51377600	Weak transcription	Esophagus	oesophagus
23	chr3:51376200-51377400	Enhancers	HSMMtube	muscle
24	chr3:51376200-51377600	Weak transcription	Gastric	stomach
25	chr3:51376400-51377600	Weak transcription	Right Ventricle	heart
26	chr3:51376400-51377600	Enhancers	Hela-S3	cervix
27	chr3:51376600-51377600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:51376600-51377800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:51376600-51378800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:51376600-51379400	Enhancers	NHLF	lung
31	chr3:51376800-51377400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:51376800-51377400	Enhancers	HSMM	muscle
33	chr3:51376800-51377600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:51376800-51377600	Weak transcription	Brain Angular Gyrus	brain
35	chr3:51376800-51377600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:51376800-51377600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:51376800-51377800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:51376800-51378400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:51376800-51378800	Enhancers	Aorta	Aorta
40	chr3:51376800-51379200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
42	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:51377000-51377400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:51377000-51377400	Weak transcription	Stomach Mucosa	stomach
45	chr3:51377000-51377600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:51377000-51377600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:51377000-51377600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:51377000-51377600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:51377000-51377600	Weak transcription	Brain Anterior Caudate	brain
50	chr3:51377000-51377600	Enhancers	HMEC	breast

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