Variant report

Variant	rs6909008
Chromosome Location	chr6:37758876-37758877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:50258702..50259774-chr6:37758614..37759901,5	K562	blood:
2	chr6:37752957..37754928-chr6:37756954..37759189,2	K562	blood:
3	chr6:37758354..37761850-chr6:37786421..37788597,3	K562	blood:
4	chr6:37756866..37759341-chr6:37763585..37765183,2	K562	blood:
5	chr6:37709546..37710466-chr6:37757585..37758878,3	MCF-7	breast:
6	chr6:37757989..37761183-chr6:37784912..37786796,3	MCF-7	breast:
7	chr6:37756505..37762867-chr6:37772774..37778127,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225945	Chromatin interaction
ENSG00000156639	Chromatin interaction

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

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

rs_ID	r²[population]
rs11757086	0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs11757695	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17512095	0.93[ASN][1000 genomes]
rs17641690	0.93[ASN][1000 genomes]
rs55753048	0.93[ASN][1000 genomes]
rs57416513	0.93[ASN][1000 genomes]
rs60672298	0.93[ASN][1000 genomes]
rs60943435	0.93[ASN][1000 genomes]
rs60977329	0.93[ASN][1000 genomes]
rs61125348	0.93[ASN][1000 genomes]
rs67979687	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910601	0.93[ASN][1000 genomes]
rs72849350	0.93[ASN][1000 genomes]
rs72849354	0.93[ASN][1000 genomes]
rs72849359	0.86[ASN][1000 genomes]
rs72849369	0.93[ASN][1000 genomes]
rs7747199	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7767466	1.00[JPT][hapmap];0.93[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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6909008	MTCH1	cis	cerebellum	SCAN
rs6909008	GLP1R	cis	cerebellum	SCAN
rs6909008	BTBD9	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37753200-37759000	Weak transcription	Right Atrium	heart
2	chr6:37755200-37759000	Weak transcription	Fetal Intestine Large	intestine
3	chr6:37755400-37759000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:37758000-37759600	Enhancers	Fetal Brain Male	brain
5	chr6:37758000-37759800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:37758000-37759800	Enhancers	Liver	Liver
7	chr6:37758200-37759000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:37758200-37759600	Enhancers	Ovary	ovary
9	chr6:37758200-37759800	Enhancers	Pancreas	Pancrea
10	chr6:37758200-37760000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:37758400-37759600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:37758400-37759800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:37758400-37759800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:37758400-37759800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr6:37758400-37759800	Enhancers	Stomach Mucosa	stomach
16	chr6:37758600-37759000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:37758600-37759200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:37758600-37759200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr6:37758600-37759600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:37758600-37759600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:37758600-37759600	Enhancers	Brain Angular Gyrus	brain
22	chr6:37758600-37759800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:37758600-37759800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:37758600-37759800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:37758600-37759800	Enhancers	Brain Cingulate Gyrus	brain
26	chr6:37758600-37759800	Enhancers	Brain Substantia Nigra	brain
27	chr6:37758600-37759800	Enhancers	Fetal Brain Female	brain
28	chr6:37758600-37759800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr6:37758600-37759800	Enhancers	HMEC	breast
30	chr6:37758600-37759800	Enhancers	NHEK	skin
31	chr6:37758600-37760000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:37758600-37760000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:37758600-37760000	Enhancers	NHLF	lung
34	chr6:37758600-37760000	Enhancers	Osteobl	bone
35	chr6:37758600-37760600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr6:37758600-37761400	Enhancers	NHDF-Ad	bronchial
37	chr6:37758600-37762600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:37758800-37759000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:37758800-37759000	Enhancers	Stomach Smooth Muscle	stomach
40	chr6:37758800-37759200	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr6:37758800-37759200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:37758800-37759200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:37758800-37759200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:37758800-37759200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:37758800-37759200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr6:37758800-37759200	Flanking Active TSS	A549	lung
47	chr6:37758800-37759200	Enhancers	GM12878-XiMat	blood
48	chr6:37758800-37759200	Flanking Active TSS	Hela-S3	cervix
49	chr6:37758800-37759200	Flanking Active TSS	HepG2	liver
50	chr6:37758800-37759200	Enhancers	HSMMtube	muscle

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