Variant report

Variant	rs56128116
Chromosome Location	chr3:156385733-156385734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156364332..156366414-chr3:156385028..156387855,2	MCF-7	breast:
2	chr3:156384119..156388903-chr3:156389462..156394403,8	MCF-7	breast:
3	chr3:156318948..156323685-chr3:156384396..156387913,5	K562	blood:
4	chr3:156384550..156386787-chr3:156850592..156853401,2	K562	blood:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513495	0.87[EUR][1000 genomes]
rs12636629	0.80[EUR][1000 genomes]
rs1367312	0.93[EUR][1000 genomes]
rs1529581	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17373227	0.92[EUR][1000 genomes]
rs41366145	0.80[EUR][1000 genomes]
rs4364127	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55686038	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56152727	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56245561	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56354026	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56357051	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56836190	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56960846	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57483705	0.80[EUR][1000 genomes]
rs58263861	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58822703	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59689193	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60032002	0.82[ASN][1000 genomes]
rs60178381	1.00[ASN][1000 genomes]
rs73012038	0.87[EUR][1000 genomes]
rs73012046	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73013957	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019737	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019748	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019749	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891463	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs919520	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56128116	LINC00886	cis	Thyroid	GTEx
rs56128116	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs56128116	LINC00886	cis	Heart Left Ventricle	GTEx
rs56128116	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156377400-156386000	Weak transcription	Psoas Muscle	Psoas
2	chr3:156382400-156388000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:156382600-156386200	Weak transcription	Fetal Kidney	kidney
4	chr3:156382600-156387000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:156382600-156387000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:156382600-156391600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:156383000-156386000	Weak transcription	Primary T cells from cord blood	blood
8	chr3:156383000-156386000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:156383000-156386200	Weak transcription	HSMMtube	muscle
10	chr3:156383000-156386800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:156383000-156391400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:156383200-156386200	Weak transcription	Fetal Lung	lung
13	chr3:156383200-156388000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr3:156383400-156385800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:156383400-156386000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:156383400-156386000	Weak transcription	NHLF	lung
17	chr3:156383600-156386000	Weak transcription	HSMM	muscle
18	chr3:156383600-156386000	Weak transcription	Osteobl	bone
19	chr3:156383600-156387800	Weak transcription	HUVEC	blood vessel
20	chr3:156383600-156390600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:156383800-156386000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:156383800-156386000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:156383800-156386000	Weak transcription	K562	blood
24	chr3:156383800-156386000	Weak transcription	NHDF-Ad	bronchial
25	chr3:156384000-156386000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:156384000-156386000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:156384200-156386000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:156384200-156386000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:156384200-156391400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:156384200-156391400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:156384400-156385800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:156384600-156386000	Weak transcription	Liver	Liver
33	chr3:156385000-156385800	Enhancers	GM12878-XiMat	blood
34	chr3:156385000-156386200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr3:156385200-156386600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:156385200-156386800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr3:156385600-156385800	Enhancers	Stomach Mucosa	stomach
38	chr3:156385600-156386000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr3:156385600-156386000	Enhancers	Hela-S3	cervix
40	chr3:156385600-156386000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr3:156385600-156386200	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr3:156385600-156386400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:156385600-156386400	Enhancers	Primary B cells from peripheral blood	blood
44	chr3:156385600-156386400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:156385600-156386400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:156385600-156386600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:156385600-156386600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr3:156385600-156386800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:156385600-156386800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:156385600-156386800	Enhancers	Small Intestine	intestine

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