Variant report

Variant	rs4677814
Chromosome Location	chr3:194865476-194865477
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	TBP	chr3:194865336-194865509	GM12878	blood:	n/a	n/a
2	REST	chr3:194865423-194865985	H1-neurons	neurons:	n/a	chr3:194865518-194865531
3	SPI1	chr3:194865222-194865632	GM12891	blood:	n/a	n/a
4	IRF1	chr3:194865280-194865589	K562	blood:	n/a	chr3:194865417-194865431 chr3:194865417-194865427 chr3:194865421-194865435 chr3:194865422-194865436 chr3:194865422-194865433 chr3:194865423-194865437 chr3:194865422-194865435 chr3:194865423-194865433 chr3:194865422-194865435 chr3:194865415-194865435 chr3:194865419-194865433
5	RUNX3	chr3:194865197-194865528	GM12878	blood:	n/a	n/a
6	RUNX3	chr3:194865240-194865684	GM12878	blood:	n/a	n/a
7	SPI1	chr3:194865080-194865810	GM12878	blood:	n/a	n/a
8	SPI1	chr3:194865257-194865630	GM12878	blood:	n/a	n/a
9	SPI1	chr3:194865219-194865602	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194825282..194827537-chr3:194865128..194866939,2	K562	blood:
2	chr3:194864066..194866570-chr3:194866869..194868881,2	K562	blood:

Variant related genes	Relation type
XXYLT1-AS2	TF binding region
ENSG00000230266	Chromatin interaction
ENSG00000244314	Chromatin interaction

Extended variants
information (count: 51 )
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];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10433329	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10433330	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10933700	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10933701	0.93[AMR][1000 genomes]
rs12491661	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491663	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2004553	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2088040	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2088041	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2410844	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2410846	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28613110	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4677662	1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4677811	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59556963	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59834989	0.84[AMR][1000 genomes]
rs60528401	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6437460	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767234	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs6799346	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73206633	0.82[AMR][1000 genomes]
rs73206646	0.83[EUR][1000 genomes]
rs73206648	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73206650	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73206651	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7628775	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]
rs7632126	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7637593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[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]
rs7653312	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[MEX][hapmap]
rs7653355	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs903309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs903311	0.88[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9809570	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9825521	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9882160	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4677814	PIGX	cis	cerebellum	SCAN
rs4677814	LOC348840	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
2	chr3:194841400-194868800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:194846600-194868400	Weak transcription	HepG2	liver
4	chr3:194847200-194868200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:194852400-194868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:194854600-194865800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:194854600-194866200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:194854600-194868400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:194854600-194868600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:194854600-194871000	Weak transcription	Fetal Brain Female	brain
11	chr3:194854800-194868400	Weak transcription	NHLF	lung
12	chr3:194855400-194868800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:194858000-194866000	Enhancers	Placenta	Placenta
14	chr3:194858600-194866800	Weak transcription	Gastric	stomach
15	chr3:194860400-194868200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:194860400-194868400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:194860600-194868400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:194860800-194866800	Weak transcription	Right Atrium	heart
19	chr3:194860800-194870200	Weak transcription	Right Ventricle	heart
20	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
21	chr3:194861200-194872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:194861600-194870800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:194861800-194868200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:194861800-194868200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:194861800-194868200	Weak transcription	Adipose Nuclei	Adipose
26	chr3:194861800-194869000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:194861800-194870800	Weak transcription	Aorta	Aorta
28	chr3:194861800-194871000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:194861800-194871200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:194861800-194872800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:194861800-194875000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:194862200-194866200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:194862200-194867200	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:194862200-194868600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:194862200-194869200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:194862400-194870600	Weak transcription	Osteobl	bone
37	chr3:194862400-194897800	Weak transcription	Dnd41	blood
38	chr3:194862600-194869200	Weak transcription	Fetal Intestine Small	intestine
39	chr3:194862800-194866800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:194862800-194866800	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:194862800-194868400	Weak transcription	Primary T cells from cord blood	blood
42	chr3:194863000-194865800	Weak transcription	Brain Substantia Nigra	brain
43	chr3:194863000-194868400	Weak transcription	Esophagus	oesophagus
44	chr3:194863000-194869200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:194863000-194869400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:194863200-194866400	Weak transcription	HUVEC	blood vessel
47	chr3:194863200-194867800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:194863600-194868400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:194863800-194870200	Weak transcription	Ovary	ovary
50	chr3:194864000-194866800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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