Variant report

Variant	rs240771
Chromosome Location	chr6:101009823-101009824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101004586..101006305-chr6:101009165..101010725,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1006399	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs240762	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240765	0.83[EUR][1000 genomes]
rs240766	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240769	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs240770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240772	0.83[EUR][1000 genomes]
rs240773	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240774	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs240776	0.84[EUR][1000 genomes]
rs240780	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240783	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240784	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240787	0.91[ASN][1000 genomes]
rs240788	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7452753	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9377085	0.83[CHB][hapmap]
rs9386193	0.95[ASN][1000 genomes]
rs9485165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997229	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv886444	chr6:100961198-101084946	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv604263	chr6:100980874-101078718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv463986	chr6:100995048-101084946	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv604264	chr6:100995048-101084946	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1028016	chr6:101001055-101158822	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv886445	chr6:101004751-101240763	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs240771	ASCC3	cis	brain	BrainEAC

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100960800-101035000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:100964200-101020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:100965200-101011400	Weak transcription	Pancreas	Pancrea
4	chr6:100965600-101033600	Weak transcription	Ovary	ovary
5	chr6:100978600-101019400	Weak transcription	HMEC	breast
6	chr6:100979800-101018200	Weak transcription	Primary T cells from cord blood	blood
7	chr6:100988000-101019000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:100988200-101018800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:100988200-101035000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:100988200-101035000	Weak transcription	GM12878-XiMat	blood
11	chr6:100988800-101034200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr6:100989000-101018400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:100990600-101018200	Weak transcription	Left Ventricle	heart
14	chr6:100996800-101016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:100997600-101017000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:100997800-101015400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:100997800-101018000	Weak transcription	Dnd41	blood
18	chr6:100998200-101015800	Weak transcription	Primary B cells from cord blood	blood
19	chr6:101001000-101034000	Weak transcription	Fetal Intestine Large	intestine
20	chr6:101001400-101020000	Weak transcription	Fetal Brain Male	brain
21	chr6:101001600-101010400	Weak transcription	Fetal Intestine Small	intestine
22	chr6:101001600-101034000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:101002000-101033600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:101002400-101027200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:101002600-101013400	Weak transcription	Liver	Liver
26	chr6:101005000-101023400	Weak transcription	Placenta	Placenta
27	chr6:101005200-101033600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:101005400-101015800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:101005400-101018200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:101006200-101035400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:101007400-101033600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:101008800-101033600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:101009000-101013600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:101009000-101014000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:101009000-101018000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:101009000-101018000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:101009000-101018200	Weak transcription	HSMM	muscle
38	chr6:101009000-101033600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:101009000-101034600	Weak transcription	NH-A	brain
40	chr6:101009000-101035000	Weak transcription	NHDF-Ad	bronchial
41	chr6:101009000-101035200	Weak transcription	Osteobl	bone
42	chr6:101009000-101065600	Weak transcription	NHEK	skin
43	chr6:101009200-101017800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:101009200-101018000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:101009600-101017600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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