Variant report

Variant	rs3799601
Chromosome Location	chr6:167001776-167001777
allele	C/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	REST	chr6:167001166-167002860	HL-60	blood:	n/a	chr6:167002009-167002029
2	TBL1XR1	chr6:167001489-167001808	GM12878	blood:	n/a	n/a
3	NFYB	chr6:167001708-167001892	GM12878	blood:	n/a	chr6:167001773-167001783
4	TCF12	chr6:167001549-167001948	GM12878	blood:	n/a	n/a
5	FOXM1	chr6:167001391-167002055	GM12878	blood:	n/a	n/a
6	RUNX3	chr6:167001099-167001936	GM12878	blood:	n/a	n/a
7	TCF12	chr6:167001544-167001989	GM12878	blood:	n/a	n/a
8	REST	chr6:167001593-167001873	PFSK-1	brain:	n/a	n/a
9	IRF4	chr6:167001486-167001888	GM12878	blood:	n/a	n/a
10	PAX5	chr6:167001475-167001882	GM12878	blood:	n/a	n/a
11	NFATC1	chr6:167001493-167001937	GM12878	blood:	n/a	n/a
12	ATF2	chr6:167001393-167001971	GM12878	blood:	n/a	n/a
13	WRNIP1	chr6:167001309-167001841	GM12878	blood:	n/a	n/a
14	REST	chr6:167001559-167001851	GM12878	blood:	n/a	n/a
15	CTCF	chr6:167001763-167001869	GM12878	blood:	n/a	chr6:167001819-167001832
16	REST	chr6:167001544-167002060	GM12878	blood:	n/a	chr6:167002009-167002029
17	RELA	chr6:167001189-167002864	GM10847	blood:	n/a	n/a
18	SPI1	chr6:167001515-167001858	GM12878	blood:	n/a	chr6:167001694-167001707
19	REST	chr6:167001596-167001892	SK-N-SH	brain:	n/a	n/a
20	TCF3	chr6:167001607-167001892	GM12878	blood:	n/a	n/a
21	REST	chr6:167001528-167001790	Hela-S3	cervix:	n/a	n/a
22	BHLHE40	chr6:167001637-167001815	GM12878	blood:	n/a	n/a
23	MAZ	chr6:167001188-167001858	GM12878	blood:	n/a	chr6:167001220-167001229
24	SPI1	chr6:167001170-167002630	GM12878	blood:	n/a	chr6:167001694-167001707
25	ELK1	chr6:167001257-167001842	GM12878	blood:	n/a	n/a
26	REST	chr6:167001562-167001831	K562	blood:	n/a	n/a
27	REST	chr6:167001632-167001916	H1-hESC	embryonic stem cell:	n/a	n/a
28	IKZF1	chr6:167001551-167001836	GM12878	blood:	n/a	n/a
29	STAT3	chr6:167001272-167001846	GM12878	blood:	n/a	chr6:167001298-167001305
30	SIN3A	chr6:167001667-167001804	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:167000381-167003269	GM12891	blood:	n/a	n/a
32	REST	chr6:167001179-167002028	GM12878	blood:	n/a	n/a
33	REST	chr6:167001583-167001912	H1-hESC	embryonic stem cell:	n/a	n/a
34	REST	chr6:167001562-167001861	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:167000300-167002507	Raji	blood:	n/a	n/a
36	STAT5A	chr6:167001552-167002019	GM12878	blood:	n/a	n/a
37	PAX5	chr6:167001532-167001819	GM12878	blood:	n/a	n/a
38	RELA	chr6:167001136-167002056	GM18951	blood:	n/a	n/a
39	TCF3	chr6:167001510-167001957	GM12878	blood:	n/a	n/a
40	STAT1	chr6:167001257-167001802	GM12878	blood:	n/a	chr6:167001298-167001305
41	REST	chr6:167001644-167001805	Hela-S3	cervix:	n/a	n/a
42	NFIC	chr6:167001123-167001910	GM12878	blood:	n/a	n/a
43	NRF1	chr6:167001524-167001893	GM12878	blood:	n/a	n/a
44	SPI1	chr6:167001587-167001844	GM12878	blood:	n/a	chr6:167001694-167001707
45	SPI1	chr6:167001477-167001924	GM12891	blood:	n/a	chr6:167001694-167001707
46	SPI1	chr6:167001489-167001936	GM12891	blood:	n/a	chr6:167001694-167001707
47	ZNF143	chr6:167001292-167001802	GM12878	blood:	n/a	n/a
48	SMC3	chr6:167001372-167001814	GM12878	blood:	n/a	n/a
49	SPI1	chr6:167001462-167001953	HL-60	blood:	n/a	chr6:167001694-167001707
50	RUNX3	chr6:167001089-167001958	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FAM103A2P	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12528284	0.89[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12661452	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2032544	0.89[CHB][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2032545	0.89[CHB][hapmap];0.90[EUR][1000 genomes]
rs34324183	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35574615	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35798186	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799579	0.89[CHB][hapmap]
rs3799581	0.89[CHB][hapmap];0.90[EUR][1000 genomes]
rs3799582	0.89[CHB][hapmap];0.90[EUR][1000 genomes]
rs3799589	0.89[CHB][hapmap];0.92[EUR][1000 genomes]
rs3799590	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799591	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799592	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799593	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799594	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3799595	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799616	0.82[JPT][hapmap]
rs3823196	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3823197	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3823198	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs3823204	0.82[JPT][hapmap]
rs6907098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6907443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs733591	0.83[ASN][1000 genomes]
rs763193	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs9295356	0.89[CHB][hapmap];0.90[EUR][1000 genomes]
rs9347138	0.89[CHB][hapmap]
rs9348149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9355586	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs9356491	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9356493	0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9356494	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9366029	0.81[ASN][1000 genomes]
rs9366031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9366033	0.88[EUR][1000 genomes]
rs960145	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv5592	chr6:166958317-167002951	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1029530	chr6:166977678-167016052	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166981800-167002400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:166986200-167002200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:166986800-167003000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:166987000-167002000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:166987200-167001800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:166989000-167011400	Weak transcription	Ovary	ovary
7	chr6:166989600-167001800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:166990600-167001800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:166993600-167003000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:166993800-167001800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:166994000-167003600	Weak transcription	Brain Germinal Matrix	brain
12	chr6:166994800-167002000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:166995000-167008400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:166995600-167002400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:166995800-167002200	Weak transcription	Right Ventricle	heart
16	chr6:166997000-167002200	Weak transcription	Pancreas	Pancrea
17	chr6:166997000-167003000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:166997200-167002000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:166997200-167002200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:166997200-167003400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:166997200-167006000	Weak transcription	Aorta	Aorta
22	chr6:166997400-167003000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:166997600-167002200	Weak transcription	HMEC	breast
24	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:166998200-167002200	Weak transcription	Left Ventricle	heart
26	chr6:166998600-167002400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:166998800-167001800	Weak transcription	Right Atrium	heart
28	chr6:166998800-167001800	Weak transcription	HSMMtube	muscle
29	chr6:166998800-167002000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:166998800-167002200	Weak transcription	NHLF	lung
31	chr6:166998800-167004000	Weak transcription	Fetal Brain Male	brain
32	chr6:166999000-167002000	Weak transcription	Osteobl	bone
33	chr6:166999000-167002200	Weak transcription	NHDF-Ad	bronchial
34	chr6:166999800-167004000	Enhancers	Fetal Thymus	thymus
35	chr6:167000000-167003000	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr6:167000000-167003400	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr6:167000000-167004400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:167000200-167003600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:167000200-167004600	Enhancers	Primary B cells from peripheral blood	blood
40	chr6:167000400-167002200	Weak transcription	Psoas Muscle	Psoas
41	chr6:167000400-167003000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:167000400-167004000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:167000400-167004200	Enhancers	Fetal Muscle Leg	muscle
44	chr6:167000400-167004200	Enhancers	Spleen	Spleen
45	chr6:167000600-167001800	Weak transcription	Brain Substantia Nigra	brain
46	chr6:167000600-167003200	Enhancers	Primary T cells from cord blood	blood
47	chr6:167000600-167003400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:167000600-167003400	Flanking Active TSS	GM12878-XiMat	blood
49	chr6:167000600-167003800	Enhancers	Fetal Kidney	kidney
50	chr6:167000600-167004200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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