Variant report

Variant	rs1478310
Chromosome Location	chr12:10534878-10534879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10534850..10537741-chr12:10540764..10542364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213809	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10743888	0.84[EUR][1000 genomes]
rs10743889	0.83[EUR][1000 genomes]
rs1382264	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1382265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1478309	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1600127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17549004	0.86[EUR][1000 genomes]
rs2045876	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2100923	0.83[EUR][1000 genomes]
rs2126888	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2126889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246809	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2255336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255353	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255364	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2417734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2617151	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617152	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2617157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2617169	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2617172	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2733840	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2733845	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2733847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2733848	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2733853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2734561	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2927561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4764430	0.87[EUR][1000 genomes]
rs6488285	0.88[EUR][1000 genomes]
rs7307721	0.88[EUR][1000 genomes]
rs7310643	0.86[EUR][1000 genomes]
rs7397310	0.84[EUR][1000 genomes]
rs7957681	0.88[EUR][1000 genomes]
rs7958658	0.88[EUR][1000 genomes]
rs7964772	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv898760	chr12:10492982-10564329	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv898761	chr12:10496724-10564329	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription 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	12 gene(s)	inside rSNPs	diseases
6	nsv1036390	chr12:10496724-10596720	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv557455	chr12:10508975-10560957	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv898762	chr12:10509383-10564329	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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	12 gene(s)	inside rSNPs	diseases
9	nsv898763	chr12:10514528-10603670	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv8914	chr12:10532300-10662676	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv557456	chr12:10532326-10698255	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1478310	KLRC4///KLRK1	Cis_1M	lymphoblastoid	RTeQTL
rs1478310	KLRK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10518400-10537000	Weak transcription	Left Ventricle	heart
2	chr12:10519600-10547800	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:10523000-10536000	Weak transcription	Ovary	ovary
4	chr12:10525400-10547200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:10527600-10538600	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:10531200-10544400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr12:10533200-10541400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:10533600-10538000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:10533600-10538600	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr12:10533800-10535800	Weak transcription	Primary T cells from cord blood	blood
11	chr12:10533800-10537800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:10533800-10538200	Weak transcription	Fetal Intestine Large	intestine
13	chr12:10533800-10539000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:10533800-10544600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:10534200-10535800	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr12:10534400-10535000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:10534600-10535200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:10534600-10535200	ZNF genes & repeats	Primary B cells from cord blood	blood
19	chr12:10534600-10535400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:10534600-10544600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:10534800-10535200	Active TSS	Primary T cells fromperipheralblood	blood
22	chr12:10534800-10535200	Strong transcription	Hela-S3	cervix
23	chr12:10534800-10535600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:10534800-10537600	Weak transcription	Osteobl	bone
25	chr12:10534800-10537800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr12:10534800-10542000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:10534800-10544400	Weak transcription	NHEK	skin
28	chr12:10534800-10548800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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