Variant report

Variant	rs10872563
Chromosome Location	chr6:144169077-144169078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144167666..144170335-chr6:144182971..144186541,3	K562	blood:
2	chr6:144162785..144166235-chr6:144168352..144172846,6	MCF-7	breast:
3	chr6:144168817..144170483-chr6:144170817..144172778,2	K562	blood:
4	chr6:144167768..144169620-chr6:144175617..144177952,2	K562	blood:
5	chr6:144167666..144170335-chr6:144182971..144186670,3	K562	blood:
6	chr6:144166292..144169400-chr6:144179889..144182426,4	K562	blood:

Variant related genes	Relation type
ENSG00000118491	Chromatin interaction
ENSG00000135521	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11155328	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1810524	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1884089	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277078	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2328508	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328509	0.81[EUR][1000 genomes]
rs3818089	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4140442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379307	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4896676	0.81[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4896678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896680	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62427458	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6918125	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6941262	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7773870	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs9484817	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9496785	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1034894	chr6:144148566-144170036	Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10872563	ADAT2	cis	cerebellum	SCAN
rs10872563	NMBR	cis	parietal	SCAN
rs10872563	C6orf103	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144165200-144169800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:144165400-144172800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:144165400-144178400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:144165600-144172200	Weak transcription	Right Atrium	heart
5	chr6:144165600-144172600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:144165600-144172600	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:144165600-144173600	Strong transcription	Placenta	Placenta
8	chr6:144165600-144175800	Weak transcription	Fetal Heart	heart
9	chr6:144165600-144175800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:144165600-144178400	Weak transcription	Stomach Mucosa	stomach
11	chr6:144165600-144186800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:144165800-144169600	Weak transcription	Small Intestine	intestine
13	chr6:144165800-144172000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:144165800-144172200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:144165800-144172200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:144165800-144172600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:144165800-144172600	Strong transcription	Fetal Stomach	stomach
18	chr6:144165800-144172800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:144165800-144172800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:144165800-144172800	Strong transcription	Osteobl	bone
21	chr6:144165800-144173600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:144165800-144173600	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:144165800-144174200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:144165800-144175400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:144166000-144169800	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr6:144166000-144170000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:144166000-144170000	Strong transcription	Fetal Brain Male	brain
28	chr6:144166000-144170000	Strong transcription	Hela-S3	cervix
29	chr6:144166000-144170400	Strong transcription	Fetal Kidney	kidney
30	chr6:144166000-144171800	Weak transcription	Psoas Muscle	Psoas
31	chr6:144166000-144172200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:144166000-144172400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:144166000-144172400	Strong transcription	HMEC	breast
34	chr6:144166000-144172400	Strong transcription	NHLF	lung
35	chr6:144166000-144172600	Strong transcription	Brain Anterior Caudate	brain
36	chr6:144166000-144172600	Strong transcription	Brain Substantia Nigra	brain
37	chr6:144166000-144172600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:144166000-144172600	Strong transcription	HSMMtube	muscle
39	chr6:144166000-144172600	Strong transcription	NH-A	brain
40	chr6:144166000-144172600	Strong transcription	NHDF-Ad	bronchial
41	chr6:144166000-144172800	Strong transcription	Fetal Brain Female	brain
42	chr6:144166000-144172800	Strong transcription	HSMM	muscle
43	chr6:144166000-144172800	Strong transcription	NHEK	skin
44	chr6:144166000-144173000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:144166000-144173000	Strong transcription	Left Ventricle	heart
46	chr6:144166000-144173400	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:144166000-144173400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:144166000-144173600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:144166000-144173600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:144166000-144173600	Strong transcription	Primary hematopoietic stem cells	blood

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