Variant report

Variant	rs412444
Chromosome Location	chr6:5004887-5004888
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	IRF1	chr6:5003726-5004893	K562	blood:	n/a	chr6:5004545-5004559
2	UBTF	chr6:5004339-5005084	K562	blood:	n/a	n/a
3	CUX1	chr6:5003914-5005064	K562	blood:	n/a	n/a
4	CTCF	chr6:5003503-5005179	A549	lung:	n/a	chr6:5004341-5004350
5	HCFC1	chr6:5003522-5005044	Hela-S3	cervix:	n/a	n/a
6	RELA	chr6:5003654-5004947	GM15510	blood:	n/a	n/a
7	RELA	chr6:5003697-5005152	GM18505	blood:	n/a	n/a
8	MYBL2	chr6:5003514-5004996	HepG2	liver:	n/a	n/a
9	MYBL2	chr6:5003624-5004913	HepG2	liver:	n/a	n/a
10	MAZ	chr6:5003560-5005590	IMR90	lung:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
11	NFIC	chr6:5003855-5004926	HepG2	liver:	n/a	n/a
12	MAX	chr6:5003595-5004965	HepG2	liver:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
13	NFIC	chr6:5003587-5004900	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:5003412-5005224	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr6:5003620-5004908	K562	blood:	n/a	n/a
16	SP1	chr6:5003594-5004887	HepG2	liver:	n/a	chr6:5004301-5004310 chr6:5004300-5004309 chr6:5004300-5004309 chr6:5004300-5004314 chr6:5004300-5004310 chr6:5004547-5004559 chr6:5004299-5004311 chr6:5004300-5004310 chr6:5004548-5004557 chr6:5004299-5004311
17	MYC	chr6:5003586-5004907	K562	blood:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
18	JUN	chr6:5003441-5005330	K562	blood:	n/a	n/a
19	POLR2A	chr6:5003618-5004897	GM12878	blood:	n/a	n/a
20	UBTF	chr6:5003660-5004935	K562	blood:	n/a	n/a
21	MTA3	chr6:5003902-5004999	GM12878	blood:	n/a	n/a
22	TBP	chr6:5003727-5004972	GM12878	blood:	n/a	n/a
23	CREB1	chr6:5003588-5004962	HepG2	liver:	n/a	n/a
24	POLR2A	chr6:5003526-5004910	PFSK-1	brain:	n/a	n/a
25	HEY1	chr6:5003653-5005221	HepG2	liver:	n/a	chr6:5004338-5004353
26	MBD4	chr6:5003921-5004962	HepG2	liver:	n/a	n/a
27	MXI1	chr6:5003515-5004893	IMR90	lung:	n/a	chr6:5003751-5003760
28	MAZ	chr6:5003652-5004980	K562	blood:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
29	ZMIZ1	chr6:5003765-5004943	K562	blood:	n/a	n/a
30	POLR2A	chr6:5003636-5005015	GM19099	blood:	n/a	n/a
31	FOXA1	chr6:5003639-5004899	HepG2	liver:	n/a	n/a
32	TEAD4	chr6:5003585-5005047	K562	blood:	n/a	n/a
33	ZBTB7A	chr6:5004271-5004905	K562	blood:	n/a	chr6:5004562-5004569 chr6:5004304-5004311
34	POLR2A	chr6:5003599-5005028	HepG2	liver:	n/a	n/a
35	BHLHE40	chr6:5003651-5004902	K562	blood:	n/a	chr6:5004328-5004344
36	POLR2A	chr6:5003577-5005411	MCF10A-Er-Src	breast:	n/a	n/a
37	MYC	chr6:5003596-5005105	K562	blood:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
38	MBD4	chr6:5003624-5005014	HepG2	liver:	n/a	n/a
39	SMC3	chr6:5003676-5004906	Hela-S3	cervix:	n/a	n/a
40	TEAD4	chr6:5003884-5005086	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:5003901-5005156	HepG2	liver:	n/a	n/a
42	RELA	chr6:5003700-5004978	GM19099	blood:	n/a	n/a
43	POLR2A	chr6:5003467-5004965	PFSK-1	brain:	n/a	n/a
44	CREB1	chr6:5003632-5004889	K562	blood:	n/a	n/a
45	MAZ	chr6:5003713-5005064	GM12878	blood:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
46	TBL1XR1	chr6:5003761-5005191	K562	blood:	n/a	n/a
47	POLR2A	chr6:5003618-5005200	HepG2	liver:	n/a	n/a
48	MAX	chr6:5003563-5004900	K562	blood:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
49	TBP	chr6:5003640-5004981	HepG2	liver:	n/a	n/a
50	POLR2A	chr6:5003667-5005016	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:5004317..5004944-chr6:5030555..5031426,2	MCF-7	breast:
2	chr6:5004268..5006268-chr6:5028632..5030855,2	K562	blood:
3	chr6:5004308..5006000-chr6:5030652..5032441,2	K562	blood:

Variant related genes	Relation type
RPP40	TF binding region
ENSG00000272142	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1246951	0.83[JPT][hapmap]
rs1246982	0.85[ASN][1000 genomes]
rs1246985	0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1246988	0.93[ASN][1000 genomes]
rs1246989	0.83[ASN][1000 genomes]
rs1246990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1246992	0.82[ASN][1000 genomes]
rs1271970	0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1615873	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1617590	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1749144	0.81[ASW][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1749158	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs275235	0.83[MEX][hapmap]
rs275242	0.83[JPT][hapmap]
rs275253	0.81[JPT][hapmap]
rs396839	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs431060	0.85[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs439795	0.85[JPT][hapmap]
rs443167	0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs563589	0.91[ASN][1000 genomes]
rs707966	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728151	0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs7744457	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs412444	FAM50B	cis	parietal	SCAN
rs412444	TUBB2B	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5003000-5005000	Active TSS	Brain Anterior Caudate	brain
2	chr6:5003200-5005000	Active TSS	A549	lung
3	chr6:5003200-5005200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:5003200-5005200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:5003400-5005200	Active TSS	Psoas Muscle	Psoas
6	chr6:5003600-5005000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr6:5003600-5005000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:5003600-5005000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:5003600-5005000	Active TSS	Brain Germinal Matrix	brain
10	chr6:5003600-5005000	Active TSS	Rectal Smooth Muscle	rectum
11	chr6:5003600-5005000	Active TSS	Right Atrium	heart
12	chr6:5003600-5005000	Active TSS	Right Ventricle	heart
13	chr6:5003800-5005000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:5003800-5005000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:5003800-5005200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr6:5003800-5005200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:5004000-5005000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:5004000-5005000	Active TSS	Fetal Muscle Trunk	muscle
19	chr6:5004400-5005000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:5004400-5005000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr6:5004400-5005000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr6:5004400-5005000	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr6:5004400-5005000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr6:5004400-5005000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr6:5004400-5005000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr6:5004400-5005000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr6:5004400-5005000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr6:5004400-5005000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr6:5004400-5005000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:5004400-5005000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr6:5004400-5005000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:5004400-5005000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:5004400-5005000	Flanking Active TSS	Liver	Liver
34	chr6:5004400-5005000	Flanking Active TSS	Fetal Stomach	stomach
35	chr6:5004400-5005000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr6:5004400-5005000	Flanking Active TSS	Thymus	Thymus
37	chr6:5004400-5005000	Flanking Active TSS	HUVEC	blood vessel
38	chr6:5004400-5005200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr6:5004400-5005200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:5004400-5005200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:5004400-5005200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr6:5004400-5005200	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr6:5004600-5005000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr6:5004600-5005000	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr6:5004600-5005000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:5004600-5005000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr6:5004600-5005000	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr6:5004600-5005000	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr6:5004600-5005000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr6:5004600-5005000	Flanking Active TSS	Brain Substantia Nigra	brain

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