Variant report

Variant	rs1322447
Chromosome Location	chr6:144618167-144618168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144613353..144615831-chr6:144616673..144618969,2	MCF-7	breast:
2	chr6:144605120..144606682-chr6:144616870..144619155,2	K562	blood:
3	chr6:144611475..144613339-chr6:144617031..144618906,2	K562	blood:

Variant related genes	Relation type
ENSG00000152818	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1474630	0.81[MEX][hapmap]
rs17073578	0.81[MEX][hapmap]
rs17073596	0.81[MEX][hapmap]
rs1967671	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2017652	0.98[ASN][1000 genomes]
rs2473131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2473133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2473134	1.00[CEU][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473138	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2473139	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2473140	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2473141	0.98[ASN][1000 genomes]
rs2473142	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2473143	0.98[ASN][1000 genomes]
rs2473144	0.98[ASN][1000 genomes]
rs2473145	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2473147	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2473148	0.83[JPT][hapmap]
rs2473149	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2473150	0.81[ASN][1000 genomes]
rs2473151	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2502628	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2502629	0.96[EUR][1000 genomes]
rs2502631	0.82[ASN][1000 genomes]
rs2502642	0.83[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	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1322447	GRM1	cis	cerebellum	SCAN
rs1322447	UTRN	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144608400-144626600	Weak transcription	Spleen	Spleen
2	chr6:144608600-144619400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:144608600-144626800	Weak transcription	Esophagus	oesophagus
4	chr6:144608600-144629800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:144608600-144631400	Weak transcription	Colonic Mucosa	Colon
6	chr6:144609200-144618200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:144609200-144618600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:144609200-144623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:144609200-144623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:144609200-144626800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:144609200-144641600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:144609600-144628800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:144609600-144629000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:144609600-144629800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:144611400-144626800	Weak transcription	Fetal Thymus	thymus
16	chr6:144612400-144624000	Weak transcription	Ovary	ovary
17	chr6:144612800-144618200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:144613800-144626800	Weak transcription	Thymus	Thymus
19	chr6:144615400-144630200	Weak transcription	Hela-S3	cervix
20	chr6:144615800-144623800	Weak transcription	HMEC	breast
21	chr6:144616200-144620200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:144616400-144618200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:144616400-144618200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr6:144616400-144618400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr6:144616400-144619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:144616400-144619800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:144616400-144648000	Weak transcription	NHEK	skin
28	chr6:144616600-144618200	Genic enhancers	Left Ventricle	heart
29	chr6:144616800-144618400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:144616800-144618400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:144616800-144618400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:144616800-144619800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:144616800-144619800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr6:144616800-144620200	Genic enhancers	HepG2	liver
35	chr6:144617000-144618400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:144617000-144618400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:144617000-144619000	Strong transcription	HSMMtube	muscle
38	chr6:144617000-144620400	Strong transcription	HSMM	muscle
39	chr6:144617000-144623800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:144617200-144618200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:144617200-144618400	Strong transcription	NHLF	lung
42	chr6:144617200-144618600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:144617200-144619600	Enhancers	Psoas Muscle	Psoas
44	chr6:144617200-144629400	Weak transcription	Placenta	Placenta
45	chr6:144617200-144636400	Weak transcription	A549	lung
46	chr6:144617400-144618200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:144617400-144618800	Enhancers	Liver	Liver
48	chr6:144617400-144619400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:144617400-144619800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:144617400-144619800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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