Variant report

Variant	rs6805930
Chromosome Location	chr3:118955611-118955612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:118954516..118958209-chr3:118958247..118961418,8	MCF-7	breast:
2	chr3:118954843..118957176-chr3:119215915..119217953,2	MCF-7	breast:
3	chr3:118952753..118957545-chr3:118958102..118959880,7	K562	blood:

Variant related genes	Relation type
ENSG00000272662	Chromatin interaction
ENSG00000121578	Chromatin interaction
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10934486	0.87[CEU][hapmap]
rs12487052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492305	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13315549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13320556	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13324867	1.00[CEU][hapmap]
rs16829413	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs2594731	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28428903	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4234656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4450805	0.87[CEU][hapmap]
rs4687841	1.00[YRI][hapmap]
rs67108505	0.81[ASN][1000 genomes]
rs6766503	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6774	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7625069	0.87[YRI][hapmap]
rs9840064	0.86[MEX][hapmap];0.87[TSI][hapmap]
rs9844248	0.95[EUR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6805930	PTPLB	cis	cerebellum	SCAN
rs6805930	GOLGB1	cis	parietal	SCAN
rs6805930	C3orf30	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:118927800-118956400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:118929200-118956200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:118929200-118956200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:118929200-118956400	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr3:118929200-118956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:118930200-118955800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:118930200-118958400	Weak transcription	Hela-S3	cervix
9	chr3:118931600-118957400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:118932600-118955800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:118944400-118955800	Strong transcription	Placenta	Placenta
12	chr3:118944400-118956200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:118945000-118956000	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr3:118945000-118956000	Strong transcription	Liver	Liver
15	chr3:118945800-118958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:118946600-118957800	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:118946800-118957200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:118947400-118955800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:118948200-118956200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr3:118948400-118958600	Weak transcription	Colonic Mucosa	Colon
21	chr3:118949000-118958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:118949000-118958400	Weak transcription	Fetal Brain Male	brain
23	chr3:118949200-118957600	Weak transcription	Fetal Heart	heart
24	chr3:118949400-118957600	Weak transcription	Right Ventricle	heart
25	chr3:118949400-118958800	Weak transcription	Lung	lung
26	chr3:118949600-118955800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:118949600-118957600	Weak transcription	Ovary	ovary
28	chr3:118949600-118958400	Weak transcription	Brain Substantia Nigra	brain
29	chr3:118949600-118958600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:118949600-118958600	Weak transcription	Brain Germinal Matrix	brain
31	chr3:118949600-118958800	Weak transcription	Gastric	stomach
32	chr3:118949800-118958800	Weak transcription	Spleen	Spleen
33	chr3:118950000-118958400	Weak transcription	Fetal Brain Female	brain
34	chr3:118950800-118956200	Strong transcription	Dnd41	blood
35	chr3:118951400-118955800	Strong transcription	Fetal Intestine Large	intestine
36	chr3:118951400-118957800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:118951600-118958800	Weak transcription	Esophagus	oesophagus
38	chr3:118952000-118958800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:118952200-118957400	Weak transcription	Thymus	Thymus
40	chr3:118952200-118957800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:118952200-118957800	Weak transcription	Small Intestine	intestine
42	chr3:118952600-118958400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:118952600-118958400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:118952800-118956000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:118952800-118958600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:118953600-118956000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:118953600-118956600	Transcr. at gene 5' and 3'	A549	lung
48	chr3:118953600-118958600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:118953800-118956000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:118953800-118956200	Strong transcription	K562	blood

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