Variant report

Variant	rs3755980
Chromosome Location	chr4:88042251-88042252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87855459..87856523-chr4:88041769..88042842,14	MCF-7	breast:
2	chr4:88041232..88043598-chr4:88048942..88050485,2	MCF-7	breast:
3	chr4:87855469..87856399-chr4:88041754..88042897,10	MCF-7	breast:
4	chr4:88023345..88024906-chr4:88040563..88042654,2	MCF-7	breast:
5	chr4:87854962..87858816-chr4:88038072..88042352,4	MCF-7	breast:
6	chr4:87926518..87929416-chr4:88041229..88043672,2	K562	blood:
7	chr4:87994063..87995021-chr4:88041972..88042770,2	MCF-7	breast:
8	chr4:88037805..88040790-chr4:88041752..88044910,3	MCF-7	breast:
9	chr4:88027865..88029794-chr4:88040230..88042955,3	MCF-7	breast:
10	chr4:87855429..87856523-chr4:88041769..88042795,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10023056	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10029915	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10032710	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516788	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs13120301	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1481947	1.00[ASW][hapmap];0.89[MEX][hapmap]
rs151450	0.88[ASN][1000 genomes]
rs151451	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1552144	1.00[ASW][hapmap];0.89[MEX][hapmap]
rs17012234	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs17012334	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs17012512	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17605615	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs17701999	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs17752307	0.84[CEU][hapmap]
rs1842685	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2035403	0.90[ASN][1000 genomes]
rs2061498	0.81[EUR][1000 genomes]
rs2280954	0.81[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap]
rs236676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs236681	0.86[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap]
rs3193672	1.00[ASW][hapmap];0.89[MEX][hapmap]
rs3733377	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3736668	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755983	1.00[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755985	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775209	0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775211	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775226	0.89[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3775228	0.86[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs4577539	1.00[ASW][hapmap];0.89[MEX][hapmap]
rs4693802	0.87[GIH][hapmap]
rs55982755	0.81[EUR][1000 genomes]
rs60695258	0.90[ASN][1000 genomes]
rs66477840	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819155	0.84[CEU][hapmap];0.94[GIH][hapmap]
rs6840258	0.83[CEU][hapmap]
rs6854749	0.84[CEU][hapmap]
rs7665282	0.84[CEU][hapmap]
rs767315	0.83[CEU][hapmap]
rs7682652	0.84[CEU][hapmap]

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	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
4	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3755980	SLC10A6	cis	cerebellum	SCAN
rs3755980	HSD17B13	cis	cerebellum	SCAN
rs3755980	HSD17B13	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:88026400-88042400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr4:88026400-88063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:88026600-88042600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:88026600-88055600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:88030000-88048800	Weak transcription	A549	lung
7	chr4:88030600-88057600	Weak transcription	Brain Germinal Matrix	brain
8	chr4:88032800-88043200	Strong transcription	Primary B cells from cord blood	blood
9	chr4:88032800-88043600	Strong transcription	Fetal Thymus	thymus
10	chr4:88032800-88059000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr4:88033000-88042800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr4:88033600-88047600	Weak transcription	HSMM	muscle
13	chr4:88034800-88043400	Weak transcription	Hela-S3	cervix
14	chr4:88035600-88056800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:88035600-88063800	Strong transcription	Primary T cells from cord blood	blood
16	chr4:88036000-88043000	Strong transcription	Primary hematopoietic stem cells	blood
17	chr4:88036400-88063600	Weak transcription	Fetal Brain Male	brain
18	chr4:88036800-88046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:88036800-88046800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:88036800-88059200	Weak transcription	Fetal Brain Female	brain
21	chr4:88037000-88042600	Weak transcription	NHLF	lung
22	chr4:88037800-88043000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:88038000-88042400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:88038000-88046200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:88038000-88046200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr4:88038200-88042600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:88038400-88046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:88038600-88042400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:88038600-88045800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:88038800-88046000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:88038800-88046800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:88038800-88047000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:88039600-88045800	Weak transcription	K562	blood
34	chr4:88039600-88046800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:88039800-88042800	Enhancers	HUVEC	blood vessel
36	chr4:88039800-88042800	Enhancers	NHDF-Ad	bronchial
37	chr4:88039800-88043800	Enhancers	Psoas Muscle	Psoas
38	chr4:88040000-88047200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:88040000-88052000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:88040200-88042800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:88040200-88043600	Genic enhancers	GM12878-XiMat	blood
42	chr4:88040400-88042800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:88040400-88042800	Flanking Active TSS	Fetal Heart	heart
44	chr4:88040400-88043800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:88040400-88043800	Strong transcription	Dnd41	blood
46	chr4:88040600-88042800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:88040600-88043800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr4:88040600-88045800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:88040800-88043800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:88040800-88045600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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