Variant report

Variant	rs412787
Chromosome Location	chr6:13280489-13280490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13266277..13270174-chr6:13278637..13282022,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFOD1-1	chr6:13279527-13281388	ENSG00000215022.3

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12203576	0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1937767	0.82[CEU][hapmap]
rs202020	0.82[JPT][hapmap]
rs202036	0.81[EUR][1000 genomes]
rs202039	0.84[CEU][hapmap]
rs202041	0.81[EUR][1000 genomes]
rs202045	0.86[YRI][hapmap]
rs202054	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs202066	0.86[CEU][hapmap]
rs2439546	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs2496143	0.86[CHD][hapmap]
rs364884	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs377704	0.82[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap]
rs381134	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3846903	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs384730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398151	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs405078	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs408639	0.81[JPT][hapmap]
rs408923	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs413120	0.84[LWK][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs417048	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421057	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441213	0.82[LWK][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap]
rs442614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445591	0.91[AFR][1000 genomes]
rs445714	0.84[LWK][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs446843	0.82[JPT][hapmap]
rs570338	0.86[CHD][hapmap]
rs629262	0.84[JPT][hapmap]
rs629728	0.82[JPT][hapmap]
rs641293	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs641688	0.86[JPT][hapmap]
rs7774863	0.84[CHD][hapmap]
rs9381915	0.82[JPT][hapmap]
rs9473896	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9473901	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs412787	ERVFRDE1	cis	cerebellum	SCAN
rs412787	RP1-257A7.5	cis	Thyroid	GTEx
rs412787	CD83	cis	parietal	SCAN
rs412787	GFOD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
2	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
3	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
6	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:13270200-13291600	Weak transcription	HSMM	muscle
9	chr6:13270400-13282000	Weak transcription	Ovary	ovary
10	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
11	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
14	chr6:13273000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:13273400-13286800	Weak transcription	Liver	Liver
16	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
17	chr6:13274000-13282600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:13274000-13283800	Weak transcription	Brain Substantia Nigra	brain
19	chr6:13274400-13286800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:13274400-13287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
22	chr6:13274600-13286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:13274600-13286800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
25	chr6:13274800-13286600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:13274800-13287000	Weak transcription	Thymus	Thymus
27	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:13275000-13282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:13275000-13285000	Weak transcription	Fetal Intestine Small	intestine
30	chr6:13275000-13286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:13275000-13287000	Weak transcription	Gastric	stomach
32	chr6:13275200-13286400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:13275600-13281000	Weak transcription	Placenta	Placenta
34	chr6:13275600-13286600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:13275600-13287000	Weak transcription	Adipose Nuclei	Adipose
36	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:13275800-13282200	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:13276000-13282800	Weak transcription	Right Ventricle	heart
39	chr6:13276000-13287400	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr6:13276200-13281400	Genic enhancers	Primary B cells from cord blood	blood
41	chr6:13276600-13281000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:13277200-13281600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:13277200-13282000	Strong transcription	Left Ventricle	heart
44	chr6:13277400-13281600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:13277400-13286200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr6:13277400-13287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:13277600-13281800	Strong transcription	Aorta	Aorta
48	chr6:13277600-13282400	Weak transcription	HepG2	liver
49	chr6:13277600-13284200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:13277800-13281000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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