Variant report

Variant	rs4946758
Chromosome Location	chr6:106959424-106959425
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	SIN3AK20	chr6:106959232-106961227	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr6:106959400-106959550	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:106959214-106961551	U87	brain:	n/a	n/a
4	POLR2A	chr6:106957807-106960924	MCF10A-Er-Src	breast:	n/a	n/a
5	CTBP2	chr6:106959338-106961073	H1-hESC	embryonic stem cell:	n/a	n/a
6	GATA3	chr6:106959365-106962481	SK-N-SH	brain:	n/a	chr6:106962075-106962087 chr6:106961183-106961200 chr6:106961187-106961208 chr6:106962073-106962089 chr6:106961192-106961202 chr6:106961194-106961204 chr6:106961194-106961201 chr6:106961194-106961201 chr6:106961194-106961201
7	WRNIP1	chr6:106959281-106959583	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:106959220-106961109	U87	brain:	n/a	n/a
9	POLR2A	chr6:106959401-106960826	U87	brain:	n/a	n/a
10	POLR2A	chr6:106959406-106959524	Hela-S3	cervix:	n/a	n/a
11	MTA3	chr6:106959166-106961075	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:106959398-106961117	GM19099	blood:	n/a	n/a
13	SMC3	chr6:106959387-106960511	Hela-S3	cervix:	n/a	n/a
14	SIN3A	chr6:106959206-106961186	H1-hESC	embryonic stem cell:	n/a	chr6:106959898-106959911 chr6:106959833-106959842
15	TEAD4	chr6:106959361-106960199	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr6:106959389-106961163	HL-60	blood:	n/a	n/a
17	POLR2A	chr6:106959401-106959969	U87	brain:	n/a	n/a
18	POLR2A	chr6:106958092-106959982	H1-neurons	neurons:	n/a	n/a
19	EBF1	chr6:106959377-106959739	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:106959067-106959883	H1-neurons	neurons:	n/a	n/a
21	SIN3AK20	chr6:106959351-106961184	PANC-1	pancreas:	n/a	n/a
22	NFIC	chr6:106959197-106959707	GM12878	blood:	n/a	n/a
23	CTCF	chr6:106959360-106959510	HBMEC	blood vessel:	n/a	n/a
24	POLR2A	chr6:106959266-106962163	Raji	blood:	n/a	n/a
25	ZNF263	chr6:106959177-106960450	HEK293-T-REx	kidney:	n/a	n/a
26	SMC3	chr6:106959295-106959500	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106955204..106959628-chr6:106966256..106969365,4	K562	blood:

Variant related genes	Relation type
AIM1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10499044	0.81[YRI][hapmap]
rs10499048	1.00[YRI][hapmap]
rs11152999	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11153000	0.84[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap]
rs11752122	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340624	0.84[ASW][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap];0.84[ASN][1000 genomes]
rs1381552	0.84[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1417357	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs4945755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62423280	0.86[EUR][1000 genomes]
rs9320172	0.91[YRI][hapmap]
rs9373876	0.86[EUR][1000 genomes]
rs9386570	0.81[YRI][hapmap]
rs9400021	0.83[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1025510	chr6:106791080-106982400	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538404	chr6:106791080-106982400	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4946758	WASF1	cis	parietal	SCAN
rs4946758	PPIL6	cis	cerebellum	SCAN
rs4946758	AIM1	cis	multi-tissue	Pritchard
rs4946758	AIM1	Cis_1M	lymphoblastoid	RTeQTL
rs4946758	FOXO3	cis	parietal	SCAN
rs4946758	AKD1	cis	parietal	SCAN
rs4946758	AIM1	cis	Liver	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106956800-106959600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr6:106957000-106962800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:106957200-106960000	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr6:106957200-106961200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:106957200-106961600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:106957200-106962800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr6:106957400-106959800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
8	chr6:106957400-106960200	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr6:106957400-106962200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:106957400-106963400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr6:106957600-106959600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr6:106957600-106959800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr6:106957600-106961000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr6:106957800-106959600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:106957800-106959800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr6:106957800-106961400	Active TSS	Right Atrium	heart
17	chr6:106958000-106960000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr6:106958000-106961000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr6:106958200-106959600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:106958200-106959800	Bivalent Enhancer	Fetal Heart	heart
21	chr6:106958200-106961200	Active TSS	NHDF-Ad	bronchial
22	chr6:106958400-106960000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:106958400-106960000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr6:106958400-106962000	Active TSS	GM12878-XiMat	blood
25	chr6:106958400-106962200	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr6:106958600-106959600	Weak transcription	Lung	lung
27	chr6:106958600-106961000	Active TSS	Aorta	Aorta
28	chr6:106958600-106961000	Active TSS	Gastric	stomach
29	chr6:106958600-106961400	Bivalent/Poised TSS	Psoas Muscle	Psoas
30	chr6:106958800-106959600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
31	chr6:106958800-106959600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
32	chr6:106958800-106959600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:106958800-106959600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:106958800-106959600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:106958800-106959600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr6:106958800-106959600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr6:106958800-106959600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:106958800-106959600	Active TSS	Colonic Mucosa	Colon
39	chr6:106958800-106959600	Active TSS	Right Ventricle	heart
40	chr6:106958800-106959600	Enhancers	Spleen	Spleen
41	chr6:106958800-106959800	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr6:106958800-106959800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
43	chr6:106958800-106960200	Flanking Active TSS	Dnd41	blood
44	chr6:106958800-106961200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:106958800-106961600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:106959000-106959600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr6:106959000-106959600	Bivalent Enhancer	Brain Germinal Matrix	brain
48	chr6:106959000-106959600	Flanking Active TSS	Hela-S3	cervix
49	chr6:106959000-106959800	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr6:106959000-106959800	Flanking Active TSS	NHLF	lung

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