Variant report

Variant	rs7628775
Chromosome Location	chr3:194851177-194851178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194846812..194848589-chr3:194850352..194852170,2	K562	blood:
2	chr3:194850925..194853976-chr3:194854035..194858487,4	K562	blood:
3	chr3:194850288..194852181-chr3:194862414..194864990,2	MCF-7	breast:
4	chr3:194839189..194844993-chr3:194846673..194851288,6	K562	blood:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction
ENSG00000265333	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10433328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10433329	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433330	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10933700	0.88[ASN][1000 genomes]
rs12491661	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491663	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2088040	0.85[ASN][1000 genomes]
rs2088041	0.85[ASN][1000 genomes]
rs2410843	0.85[ASN][1000 genomes]
rs2410844	0.85[ASN][1000 genomes]
rs2410846	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28613110	0.85[ASN][1000 genomes]
rs4677662	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs4677807	0.85[ASN][1000 genomes]
rs4677811	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4677814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59556963	0.83[ASN][1000 genomes]
rs60528401	0.88[ASN][1000 genomes]
rs6437460	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6767234	0.94[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.85[ASN][1000 genomes]
rs6799346	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73206633	0.81[ASN][1000 genomes]
rs73206646	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73206648	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73206650	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73206651	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7618901	0.85[ASN][1000 genomes]
rs7630048	0.82[ASN][1000 genomes]
rs7632126	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7637593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[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];1.00[ASN][1000 genomes]
rs7653312	0.87[CEU][hapmap];0.88[CHB][hapmap];0.87[MEX][hapmap]
rs7653355	0.88[ASN][1000 genomes]
rs903309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903311	0.88[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.85[ASN][1000 genomes]
rs9809570	0.85[ASN][1000 genomes]
rs9825521	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
13	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
15	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
17	esv996963	chr3:194845436-194854988	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7628775	PIGX	cis	cerebellum	SCAN
rs7628775	LOC348840	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194827400-194853600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:194827400-194861200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:194831600-194857400	Weak transcription	Pancreas	Pancrea
4	chr3:194832400-194853600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:194832800-194856200	Weak transcription	Primary T cells from cord blood	blood
6	chr3:194839200-194861200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:194839200-194861400	Weak transcription	Aorta	Aorta
8	chr3:194841000-194853400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
10	chr3:194841400-194868800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:194841800-194851200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:194843800-194856600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:194844600-194860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:194844800-194859800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:194845400-194852000	Weak transcription	Fetal Stomach	stomach
16	chr3:194845600-194858000	Weak transcription	Fetal Intestine Small	intestine
17	chr3:194845600-194861200	Weak transcription	Ovary	ovary
18	chr3:194846200-194851400	Weak transcription	Fetal Heart	heart
19	chr3:194846200-194851400	Weak transcription	Placenta	Placenta
20	chr3:194846200-194862400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:194846400-194851400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:194846400-194853800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:194846600-194851600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:194846600-194868400	Weak transcription	HepG2	liver
25	chr3:194846800-194854600	Weak transcription	Left Ventricle	heart
26	chr3:194847200-194868200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:194847600-194851400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:194847600-194857800	Weak transcription	Spleen	Spleen
29	chr3:194847600-194858200	Weak transcription	Adipose Nuclei	Adipose
30	chr3:194847800-194856200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:194848800-194851200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:194849000-194851400	Enhancers	Osteobl	bone
33	chr3:194849200-194851200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:194849200-194851200	Enhancers	NH-A	brain
35	chr3:194849200-194861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:194849400-194851200	Enhancers	K562	blood
37	chr3:194849400-194856000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:194849400-194857000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:194849400-194858200	Weak transcription	Lung	lung
40	chr3:194849600-194851200	Weak transcription	Fetal Kidney	kidney
41	chr3:194849600-194853400	Weak transcription	Stomach Mucosa	stomach
42	chr3:194849600-194855000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:194849600-194856200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:194849800-194853800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:194850000-194851600	Enhancers	NHEK	skin
46	chr3:194850000-194853000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:194850200-194853000	Enhancers	HMEC	breast
48	chr3:194850400-194851200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr3:194850400-194853800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:194850400-194854400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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