Variant report

Variant	rs240783
Chromosome Location	chr6:100968737-100968738
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	chr6:100967956..100970627-chr6:100970940..100972934,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1006399	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs240762	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240765	0.83[EUR][1000 genomes]
rs240766	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240769	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240770	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240771	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240772	0.82[EUR][1000 genomes]
rs240773	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240774	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs240776	0.83[EUR][1000 genomes]
rs240780	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240784	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240787	0.94[ASN][1000 genomes]
rs240788	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7452753	0.90[ASN][1000 genomes]
rs9377085	0.83[CHB][hapmap]
rs9386193	0.92[ASN][1000 genomes]
rs9485165	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997229	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[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	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	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs240783	ASCC3	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100951600-100969800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:100952800-100997400	Weak transcription	A549	lung
3	chr6:100954600-100986200	Weak transcription	Spleen	Spleen
4	chr6:100955200-100972800	Weak transcription	Right Ventricle	heart
5	chr6:100955800-100991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:100957400-100992400	Weak transcription	Small Intestine	intestine
7	chr6:100958200-100976600	Weak transcription	NHDF-Ad	bronchial
8	chr6:100958600-100974000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:100960200-100978000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:100960600-100973800	Weak transcription	HUVEC	blood vessel
11	chr6:100960600-100990200	Weak transcription	Brain Substantia Nigra	brain
12	chr6:100960800-100969400	Weak transcription	Esophagus	oesophagus
13	chr6:100960800-100970800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:100960800-100971200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:100960800-100971200	Weak transcription	Thymus	Thymus
16	chr6:100960800-100974000	Weak transcription	NH-A	brain
17	chr6:100960800-100977600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:100960800-100981000	Weak transcription	Gastric	stomach
19	chr6:100960800-100986000	Weak transcription	GM12878-XiMat	blood
20	chr6:100960800-100986200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:100960800-100986600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:100960800-100989600	Weak transcription	K562	blood
23	chr6:100960800-100989800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:100960800-101035000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:100961000-100986600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:100961000-100987200	Weak transcription	Osteobl	bone
27	chr6:100961000-100988800	Weak transcription	NHEK	skin
28	chr6:100961000-100991200	Weak transcription	HSMMtube	muscle
29	chr6:100961000-100992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:100961000-100997200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:100961200-100989000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:100961400-100986000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:100963000-100986800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:100964000-100990800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:100964200-100968800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:100964200-100986200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:100964200-101020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:100964800-100998400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:100965200-100972800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:100965200-100984000	Weak transcription	HepG2	liver
41	chr6:100965200-100986600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:100965200-100989600	Weak transcription	Aorta	Aorta
43	chr6:100965200-100990200	Weak transcription	Left Ventricle	heart
44	chr6:100965200-101000800	Weak transcription	Fetal Intestine Small	intestine
45	chr6:100965200-101011400	Weak transcription	Pancreas	Pancrea
46	chr6:100965400-100969200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:100965400-100976600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:100965400-100976600	Weak transcription	HSMM	muscle
49	chr6:100965400-100977600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:100965400-100984200	Weak transcription	Monocytes-CD14+_RO01746	blood

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