Variant report

Variant	rs41269265
Chromosome Location	chr6:27425349-27425350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27414265..27420654-chr6:27420859..27426179,12	K562	blood:
2	chr6:27420165..27423011-chr6:27423829..27426200,3	MCF-7	breast:
3	chr6:27423819..27426163-chr6:27438828..27440808,2	MCF-7	breast:
4	chr6:27283533..27286469-chr6:27424537..27427357,2	K562	blood:
5	chr6:27414915..27419456-chr6:27425103..27430538,5	MCF-7	breast:
6	chr6:27423322..27425992-chr6:27438717..27441582,2	K562	blood:
7	chr6:27424492..27429899-chr6:27438525..27441854,6	K562	blood:

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484399	0.89[EUR][1000 genomes]
rs13191227	0.92[EUR][1000 genomes]
rs13191474	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195636	0.91[EUR][1000 genomes]
rs13196692	0.92[EUR][1000 genomes]
rs13202775	0.83[EUR][1000 genomes]
rs13207689	0.91[EUR][1000 genomes]
rs13209332	0.91[EUR][1000 genomes]
rs13218537	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28360634	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34071253	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34105070	0.83[EUR][1000 genomes]
rs34196306	0.96[EUR][1000 genomes]
rs34332556	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34573979	0.94[EUR][1000 genomes]
rs34613987	0.87[EUR][1000 genomes]
rs34864796	0.87[EUR][1000 genomes]
rs34953377	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34965299	0.91[EUR][1000 genomes]
rs35120058	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35716472	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35848276	0.91[EUR][1000 genomes]
rs35984974	0.91[EUR][1000 genomes]
rs56401801	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58616630	0.94[EUR][1000 genomes]
rs66785117	0.91[EUR][1000 genomes]
rs66841633	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67240003	0.87[EUR][1000 genomes]
rs67859638	0.91[EUR][1000 genomes]
rs6904596	0.87[EUR][1000 genomes]
rs6918792	0.86[EUR][1000 genomes]
rs71537559	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72839477	0.87[EUR][1000 genomes]
rs7749305	0.87[EUR][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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
3	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41269265	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs41269265	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs41269265	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27412600-27438000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:27413600-27425600	ZNF genes & repeats	Fetal Brain Female	brain
3	chr6:27414000-27425600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr6:27414200-27430600	ZNF genes & repeats	Liver	Liver
5	chr6:27414400-27432000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr6:27415400-27425400	ZNF genes & repeats	Brain Germinal Matrix	brain
7	chr6:27415400-27425800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
8	chr6:27415400-27430000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:27415400-27438600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:27415600-27425400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
11	chr6:27415600-27425400	ZNF genes & repeats	HSMMtube	muscle
12	chr6:27415600-27425600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:27415600-27425600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr6:27415600-27425600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:27415600-27427400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
16	chr6:27415600-27429800	ZNF genes & repeats	Dnd41	blood
17	chr6:27415600-27430000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:27415600-27430000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:27415600-27430200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
20	chr6:27415800-27425800	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr6:27415800-27430000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:27415800-27430200	ZNF genes & repeats	Primary B cells from cord blood	blood
23	chr6:27415800-27434000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr6:27416000-27425400	ZNF genes & repeats	Fetal Muscle Leg	muscle
25	chr6:27416000-27432400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:27416200-27425600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:27416200-27425800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
28	chr6:27416200-27432600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:27416400-27428000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
30	chr6:27416600-27429200	ZNF genes & repeats	HSMM	muscle
31	chr6:27416800-27429400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
32	chr6:27416800-27430600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
33	chr6:27417200-27425600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:27417200-27432600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:27417400-27425400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:27417400-27427400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr6:27417600-27425400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
38	chr6:27417600-27425600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:27417600-27427000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr6:27417600-27430000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
41	chr6:27417800-27425400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
42	chr6:27417800-27425400	ZNF genes & repeats	Fetal Heart	heart
43	chr6:27417800-27425400	ZNF genes & repeats	HUVEC	blood vessel
44	chr6:27417800-27425600	ZNF genes & repeats	K562	blood
45	chr6:27417800-27425800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
46	chr6:27417800-27429400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
47	chr6:27418000-27430200	ZNF genes & repeats	GM12878-XiMat	blood
48	chr6:27418200-27425400	ZNF genes & repeats	NHEK	skin
49	chr6:27418200-27425600	ZNF genes & repeats	Fetal Kidney	kidney
50	chr6:27418200-27425600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum

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