Variant report

Variant	rs12190637
Chromosome Location	chr6:86297719-86297720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86294224..86298589-chr6:86301078..86306001,4	MCF-7	breast:
2	chr6:86296961..86299849-chr6:86387985..86389629,2	K562	blood:
3	chr6:86294754..86298777-chr6:86299293..86305225,6	MCF-7	breast:
4	chr6:86296828..86298833-chr6:86383928..86385738,2	K562	blood:

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10455447	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17440806	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs17440948	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs17819627	1.00[JPT][hapmap]
rs6454477	0.93[ASN][1000 genomes]

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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
5	esv3351743	chr6:86286282-86308720	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12190637	SNORD50A	cis	cerebellum	SCAN
rs12190637	RIPPLY2	cis	cerebellum	SCAN
rs12190637	SNORD50A	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
2	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
3	chr6:86278200-86302600	Weak transcription	Ovary	ovary
4	chr6:86280000-86301400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:86281400-86301600	Weak transcription	Fetal Thymus	thymus
6	chr6:86286600-86302000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:86288200-86301400	Weak transcription	Fetal Heart	heart
8	chr6:86289200-86301000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:86290000-86300800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:86290000-86301000	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:86290200-86301800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:86290400-86301400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:86290400-86302400	Weak transcription	Placenta	Placenta
14	chr6:86290800-86301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:86290800-86302000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:86291000-86302000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:86291000-86302000	Weak transcription	HSMM	muscle
18	chr6:86291000-86302600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:86291200-86298600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:86291200-86300600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:86291200-86301000	Weak transcription	Primary T cells from cord blood	blood
22	chr6:86291200-86301200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:86291200-86301200	Weak transcription	Hela-S3	cervix
24	chr6:86291200-86301200	Weak transcription	NHEK	skin
25	chr6:86291200-86301400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:86291200-86301800	Weak transcription	HUVEC	blood vessel
27	chr6:86291200-86302600	Weak transcription	Pancreas	Pancrea
28	chr6:86291200-86302600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:86291200-86302800	Weak transcription	Gastric	stomach
30	chr6:86291400-86300400	Weak transcription	A549	lung
31	chr6:86292000-86298600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:86292000-86299800	Weak transcription	HepG2	liver
33	chr6:86292000-86300400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:86292000-86300600	Weak transcription	K562	blood
35	chr6:86292000-86301000	Weak transcription	Primary B cells from cord blood	blood
36	chr6:86292000-86301200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:86292000-86301800	Weak transcription	NHDF-Ad	bronchial
38	chr6:86293800-86301000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:86294000-86301800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:86294600-86301200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:86294800-86298400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr6:86294800-86299400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:86295000-86298600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:86295000-86301400	Weak transcription	Dnd41	blood
45	chr6:86295600-86300600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:86295600-86301000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:86295600-86301000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:86295800-86301800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:86296000-86300400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:86296000-86300800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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