Variant report

Variant	rs4712908
Chromosome Location	chr6:25320920-25320921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12055533	0.85[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12196702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1989206	0.84[ASN][1000 genomes]
rs2143022	0.84[ASN][1000 genomes]
rs2252012	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2328878	0.87[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2690109	0.99[ASN][1000 genomes]
rs2690115	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2690120	0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2690123	0.83[ASN][1000 genomes]
rs2690125	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2690129	0.85[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2690131	0.81[ASN][1000 genomes]
rs2744290	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2744296	0.83[ASN][1000 genomes]
rs2744299	0.84[ASN][1000 genomes]
rs2744302	0.99[ASN][1000 genomes]
rs2744303	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9348670	0.84[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9356973	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9358850	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9358851	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9379751	0.87[CHD][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9467465	0.87[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4712908	GPR146	trans	cerebellum	SCAN
rs4712908	HIST1H2BI	cis	parietal	SCAN
rs4712908	HIST1H2BL	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
2	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
3	chr6:25312000-25324200	Weak transcription	Esophagus	oesophagus
4	chr6:25312000-25324200	Weak transcription	Pancreas	Pancrea
5	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:25313800-25322800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:25313800-25325800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:25313800-25326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:25314000-25325000	Weak transcription	Placenta	Placenta
11	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:25315800-25324200	Weak transcription	Hela-S3	cervix
13	chr6:25316200-25326800	Weak transcription	Gastric	stomach
14	chr6:25316400-25326600	Weak transcription	Fetal Kidney	kidney
15	chr6:25316600-25324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:25317200-25324200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:25317200-25324200	Weak transcription	Aorta	Aorta
18	chr6:25317400-25324000	Weak transcription	Fetal Intestine Large	intestine
19	chr6:25318000-25321600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:25318400-25321200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr6:25318400-25321200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:25318400-25321600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:25318600-25324200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:25318600-25324400	Weak transcription	Lung	lung
25	chr6:25319000-25324200	Weak transcription	Ovary	ovary
26	chr6:25319000-25324200	Weak transcription	Right Atrium	heart
27	chr6:25319200-25324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:25319400-25324200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:25319400-25324200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:25319600-25321200	Enhancers	Small Intestine	intestine
31	chr6:25319800-25324200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:25320000-25321200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:25320200-25321000	Enhancers	H9 Cell Line	embryonic stem cell
34	chr6:25320200-25321000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:25320200-25321600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:25320200-25321600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr6:25320200-25321600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr6:25320200-25321600	Enhancers	HSMMtube	muscle
39	chr6:25320400-25321000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr6:25320400-25321000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:25320400-25321000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:25320400-25321200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:25320400-25321200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr6:25320600-25321000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:25320600-25321000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:25320600-25321000	Enhancers	A549	lung
47	chr6:25320600-25321000	Enhancers	HSMM	muscle
48	chr6:25320600-25321000	Enhancers	NHLF	lung
49	chr6:25320600-25321200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:25320600-25321600	Enhancers	H1 Cell Line	embryonic stem cell

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