Variant report

Variant	rs3747771
Chromosome Location	chr6:24425671-24425672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24424515..24426613-chr6:24427739..24429764,2	K562	blood:
2	chr6:24424501..24427723-chr6:24493880..24496586,3	MCF-7	breast:
3	chr6:24423442..24426628-chr6:24427479..24429179,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1054862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889240	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889242	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889253	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16901722	0.93[CHB][hapmap];0.91[ASN][1000 genomes]
rs17306130	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298060	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45448393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45478094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45482500	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45574139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45590133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461006	0.92[EUR][1000 genomes];0.95[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	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3747771	GPLD1	cis	Esophagus Muscularis	GTEx
rs3747771	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24405000-24427600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:24405400-24426400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:24405400-24427000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:24405400-24427200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:24405400-24427200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:24405400-24427600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:24405400-24427600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr6:24405400-24428200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:24405800-24426400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:24406000-24427000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:24406400-24427600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:24406600-24427400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:24407400-24426600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:24407400-24427200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:24407600-24426400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr6:24407600-24426400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr6:24407600-24426600	Strong transcription	Placenta	Placenta
19	chr6:24407600-24427000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr6:24407600-24427600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:24407600-24428200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr6:24407800-24426600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:24407800-24427600	Strong transcription	Fetal Thymus	thymus
24	chr6:24408000-24426800	Strong transcription	Osteobl	bone
25	chr6:24408000-24427800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:24408400-24426000	Strong transcription	HepG2	liver
27	chr6:24409000-24427000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:24409200-24427600	Strong transcription	Dnd41	blood
29	chr6:24410000-24430800	Strong transcription	Left Ventricle	heart
30	chr6:24410600-24426000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:24410600-24426600	Strong transcription	Fetal Intestine Large	intestine
32	chr6:24411800-24426000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:24412200-24427600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:24412200-24427600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr6:24412200-24427600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr6:24412200-24427600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:24412200-24428200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:24412400-24426000	Strong transcription	Fetal Lung	lung
39	chr6:24412400-24426200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:24412400-24426200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:24412400-24426800	Strong transcription	Adipose Nuclei	Adipose
42	chr6:24412400-24427200	Strong transcription	K562	blood
43	chr6:24412400-24427600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:24412400-24427600	Strong transcription	Fetal Brain Female	brain
45	chr6:24412600-24426000	Strong transcription	Brain Substantia Nigra	brain
46	chr6:24412600-24426400	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:24412600-24426400	Strong transcription	Hela-S3	cervix
48	chr6:24412600-24426600	Strong transcription	HMEC	breast
49	chr6:24412600-24428600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:24412600-24429000	Strong transcription	Primary B cells from cord blood	blood

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