Variant report

Variant	rs2473134
Chromosome Location	chr6:144617117-144617118
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: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1322447	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]
rs1474630	0.81[MEX][hapmap]
rs17073578	0.81[MEX][hapmap]
rs17073596	0.81[MEX][hapmap]
rs1967671	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2017652	0.98[ASN][1000 genomes]
rs2473131	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473132	1.00[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2473133	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2473138	0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2473139	0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2473140	0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2473141	0.98[ASN][1000 genomes]
rs2473142	0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2473143	0.98[ASN][1000 genomes]
rs2473144	0.98[ASN][1000 genomes]
rs2473145	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2473147	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2473149	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2473150	0.81[ASN][1000 genomes]
rs2473151	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2502628	0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2502629	0.94[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
rs2473134	GRM1	cis	cerebellum	SCAN
rs2473134	UTRN	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144608400-144626600	Weak transcription	Spleen	Spleen
2	chr6:144608600-144617200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:144608600-144617200	Weak transcription	Gastric	stomach
4	chr6:144608600-144617800	Weak transcription	Stomach Mucosa	stomach
5	chr6:144608600-144619400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:144608600-144626800	Weak transcription	Esophagus	oesophagus
7	chr6:144608600-144629800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:144608600-144631400	Weak transcription	Colonic Mucosa	Colon
9	chr6:144608800-144617600	Weak transcription	Right Atrium	heart
10	chr6:144609200-144617200	Weak transcription	Fetal Intestine Small	intestine
11	chr6:144609200-144617200	Weak transcription	Psoas Muscle	Psoas
12	chr6:144609200-144617800	Weak transcription	Brain Anterior Caudate	brain
13	chr6:144609200-144617800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:144609200-144618000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:144609200-144618000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:144609200-144618200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:144609200-144618600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:144609200-144623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:144609200-144623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:144609200-144626800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:144609200-144641600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:144609400-144617600	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:144609400-144617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:144609600-144628800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:144609600-144629000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:144609600-144629800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:144610400-144617200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:144611400-144626800	Weak transcription	Fetal Thymus	thymus
29	chr6:144612400-144617800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr6:144612400-144624000	Weak transcription	Ovary	ovary
31	chr6:144612800-144618200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:144613800-144626800	Weak transcription	Thymus	Thymus
33	chr6:144614000-144617400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:144615400-144630200	Weak transcription	Hela-S3	cervix
35	chr6:144615800-144623800	Weak transcription	HMEC	breast
36	chr6:144616200-144617200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr6:144616200-144620200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:144616400-144617200	Strong transcription	Liver	Liver
39	chr6:144616400-144617200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr6:144616400-144617200	Genic enhancers	NHLF	lung
41	chr6:144616400-144617400	Strong transcription	Fetal Kidney	kidney
42	chr6:144616400-144617600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:144616400-144617600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:144616400-144617600	Strong transcription	HUVEC	blood vessel
45	chr6:144616400-144617800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr6:144616400-144617800	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:144616400-144618000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:144616400-144618000	Strong transcription	Dnd41	blood
49	chr6:144616400-144618200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:144616400-144618200	Strong transcription	Monocytes-CD14+_RO01746	blood

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