Variant report

Variant	rs881611
Chromosome Location	chr4:143327776-143327777
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	TCF7L2	chr4:143327405-143327793	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr4:143324039-143328578	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr4:143327498-143328023	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr4:143327751-143327911	MCF10A-Er-Src	breast:	n/a	n/a
5	BHLHE40	chr4:143327366-143327784	GM12878	blood:	n/a	n/a
6	MYC	chr4:143326019-143327845	MCF10A-Er-Src	breast:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
7	FOXM1	chr4:143326822-143327864	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr4:143327378-143327817	MCF10A-Er-Src	breast:	n/a	n/a
9	TEAD4	chr4:143326102-143327900	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr4:143326927-143327796	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:143327592..143330271-chr4:143378912..143381553,2	MCF-7	breast:
2	chr4:143327221..143331819-chr4:143394116..143397905,6	MCF-7	breast:
3	chr4:143327412..143330052-chr4:143383937..143385936,2	MCF-7	breast:
4	chr4:143327600..143329351-chr4:143391019..143392587,2	MCF-7	breast:
5	chr4:143326852..143329330-chr4:143520781..143523143,2	MCF-7	breast:
6	chr4:143326731..143329100-chr4:143388048..143390704,2	MCF-7	breast:
7	chr4:143326578..143329374-chr4:143334403..143336752,2	MCF-7	breast:

Variant related genes	Relation type
INPP4B	TF binding region
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10519658	0.87[LWK][hapmap]
rs1158692	0.92[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap]
rs11722756	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511267	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13128245	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13135641	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138212	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13140802	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13144939	0.92[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs1391098	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs1489577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497389	0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1497397	0.92[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs1497398	0.87[CEU][hapmap]
rs1565306	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1812174	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs1982965	0.84[LWK][hapmap]
rs1982966	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2173209	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2306913	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2635424	0.92[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs2635429	0.80[CEU][hapmap]
rs2646085	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs34830426	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35151914	0.87[ASN][1000 genomes]
rs3775703	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3775705	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775706	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775710	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775711	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822157	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6825345	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs716762	0.92[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs724131	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs72724560	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699598	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs931419	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs983767	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv968011	chr4:143325315-143333139	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs881611	LSM6	cis	cerebellum	SCAN
rs881611	C4orf49	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143320800-143328000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:143326400-143327800	Enhancers	H1 Cell Line	embryonic stem cell
3	chr4:143326400-143327800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:143326400-143327800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:143326400-143327800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:143326400-143328000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:143326400-143328600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr4:143326400-143329000	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr4:143326400-143330400	Enhancers	Hela-S3	cervix
10	chr4:143326600-143327800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:143326600-143327800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:143326600-143327800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:143326600-143327800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:143326600-143327800	Flanking Active TSS	Fetal Heart	heart
15	chr4:143326600-143327800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr4:143326600-143328200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:143326600-143328200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:143326600-143328200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr4:143326600-143328200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr4:143326600-143328200	Flanking Active TSS	Osteobl	bone
21	chr4:143326600-143328400	Flanking Active TSS	HMEC	breast
22	chr4:143326600-143328600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:143326600-143328800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:143326600-143329000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr4:143326600-143329000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr4:143326600-143329000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr4:143326600-143329000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr4:143326800-143327800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:143326800-143328000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr4:143326800-143328000	Flanking Active TSS	A549	lung
31	chr4:143326800-143328200	Enhancers	Colonic Mucosa	Colon
32	chr4:143327000-143327800	Enhancers	Fetal Stomach	stomach
33	chr4:143327000-143327800	Weak transcription	Right Ventricle	heart
34	chr4:143327000-143328000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:143327000-143328000	Enhancers	Fetal Kidney	kidney
36	chr4:143327000-143328000	Enhancers	Stomach Smooth Muscle	stomach
37	chr4:143327000-143328200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:143327000-143328200	Enhancers	Duodenum Mucosa	Duodenum
39	chr4:143327000-143328200	Enhancers	GM12878-XiMat	blood
40	chr4:143327000-143328400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:143327000-143328800	Enhancers	Stomach Mucosa	stomach
42	chr4:143327000-143329000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:143327000-143329000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr4:143327000-143329000	Enhancers	Fetal Intestine Small	intestine
45	chr4:143327000-143329000	Enhancers	Fetal Thymus	thymus
46	chr4:143327000-143329000	Enhancers	Thymus	Thymus
47	chr4:143327000-143330000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:143327000-143330000	Enhancers	HUVEC	blood vessel
49	chr4:143327000-143330400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:143327200-143328200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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