Variant report

Variant	rs4300953
Chromosome Location	chr3:194846903-194846904
allele	A/G
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	RUNX3	chr3:194846586-194847265	GM12878	blood:	n/a	chr3:194846987-194847004
2	RUNX3	chr3:194846586-194847324	GM12878	blood:	n/a	chr3:194846987-194847004
3	ELF1	chr3:194846797-194847128	GM12878	blood:	n/a	n/a
4	MTA3	chr3:194846678-194847354	GM12878	blood:	n/a	n/a
5	EBF1	chr3:194846746-194847162	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:194845075..194847856-chr3:194862075..194863679,2	K562	blood:
2	chr3:194844833..194847552-chr3:194858223..194860108,2	K562	blood:
3	chr3:194843365..194845377-chr3:194846362..194848480,3	MCF-7	breast:
4	chr3:194839189..194844993-chr3:194846673..194851288,6	K562	blood:
5	chr3:194846812..194848589-chr3:194850352..194852170,2	K562	blood:

Variant related genes	Relation type
XXYLT1	TF binding region
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1009642	0.86[CEU][hapmap];0.81[MEX][hapmap]
rs11721261	0.82[CEU][hapmap]
rs11917068	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1552893	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131876	0.86[CEU][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs2131879	0.91[CHB][hapmap];0.92[CHD][hapmap];0.88[ASN][1000 genomes]
rs2172695	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279630	0.83[AMR][1000 genomes]
rs28573813	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28756361	0.87[ASN][1000 genomes]
rs3892194	0.86[CEU][hapmap];0.81[MEX][hapmap]
rs4266129	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4645095	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677663	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4677808	0.87[ASN][1000 genomes]
rs4677810	0.86[CEU][hapmap]
rs4677812	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4989375	0.87[ASN][1000 genomes]
rs55751800	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55879118	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58370605	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60329099	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6794540	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6797160	0.91[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7612579	0.83[AMR][1000 genomes]
rs7616877	0.87[ASN][1000 genomes]
rs7639698	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7644208	0.86[CEU][hapmap];0.81[MEX][hapmap]
rs7646496	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7650833	0.84[CHB][hapmap]
rs874198	0.86[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs903308	0.87[ASN][1000 genomes]
rs903310	0.95[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs950257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848862	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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
rs4300953	FAM43A	cis	lymphoblastoid	seeQTL
rs4300953	RPL35A	cis	cerebellum	SCAN

Chromatin state (count:60 , 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	chr3:194834800-194850400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:194839200-194861200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:194839200-194861400	Weak transcription	Aorta	Aorta
9	chr3:194839400-194848800	Weak transcription	Lung	lung
10	chr3:194839600-194849200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:194840200-194849200	Weak transcription	Fetal Kidney	kidney
12	chr3:194840600-194849200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:194841000-194849800	Weak transcription	NHLF	lung
14	chr3:194841000-194853400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
16	chr3:194841400-194849000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:194841400-194868800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:194841800-194851200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:194843800-194856600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr3:194844000-194847600	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:194844200-194849000	Weak transcription	Dnd41	blood
22	chr3:194844400-194848800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:194844400-194849800	Weak transcription	NHDF-Ad	bronchial
24	chr3:194844600-194849400	Weak transcription	K562	blood
25	chr3:194844600-194860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:194844800-194847600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:194844800-194848000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:194844800-194848000	Enhancers	Fetal Thymus	thymus
29	chr3:194844800-194859800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:194845000-194847000	Enhancers	Right Ventricle	heart
31	chr3:194845000-194847200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr3:194845000-194847800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:194845400-194852000	Weak transcription	Fetal Stomach	stomach
34	chr3:194845600-194858000	Weak transcription	Fetal Intestine Small	intestine
35	chr3:194845600-194861200	Weak transcription	Ovary	ovary
36	chr3:194845800-194850200	Enhancers	Primary B cells from peripheral blood	blood
37	chr3:194846000-194847200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr3:194846000-194847400	Enhancers	Thymus	Thymus
39	chr3:194846200-194847200	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:194846200-194848800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:194846200-194849000	Weak transcription	Right Atrium	heart
42	chr3:194846200-194851400	Weak transcription	Fetal Heart	heart
43	chr3:194846200-194851400	Weak transcription	Placenta	Placenta
44	chr3:194846200-194862400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:194846400-194847600	Enhancers	Primary B cells from cord blood	blood
46	chr3:194846400-194847600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:194846400-194847600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:194846400-194848800	Enhancers	GM12878-XiMat	blood
49	chr3:194846400-194849200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:194846400-194851400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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