Variant report

Variant	rs240780
Chromosome Location	chr6:100964147-100964148
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:100963737..100966583-chr6:100995209..100997563,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240765	0.84[EUR][1000 genomes]
rs240766	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240769	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs240770	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240771	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240772	0.83[EUR][1000 genomes]
rs240773	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240774	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs240776	0.84[EUR][1000 genomes]
rs240783	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];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240787	0.94[ASN][1000 genomes]
rs240788	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[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	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997229	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats 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	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
4	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
5	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

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100949800-100966400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:100951600-100969800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:100952600-100967600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:100952800-100997400	Weak transcription	A549	lung
5	chr6:100953000-100968400	Weak transcription	Fetal Kidney	kidney
6	chr6:100953200-100966200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:100953400-100966600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:100953400-100967400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:100954200-100966200	Strong transcription	Dnd41	blood
10	chr6:100954600-100986200	Weak transcription	Spleen	Spleen
11	chr6:100954800-100966200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:100955200-100972800	Weak transcription	Right Ventricle	heart
13	chr6:100955400-100965800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:100955600-100964200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:100955600-100965600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:100955600-100966000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:100955800-100964800	Weak transcription	Psoas Muscle	Psoas
18	chr6:100955800-100965600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:100955800-100965600	Weak transcription	Brain Angular Gyrus	brain
20	chr6:100955800-100966400	Weak transcription	Colonic Mucosa	Colon
21	chr6:100955800-100966800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:100955800-100991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:100956400-100965400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:100956800-100965400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:100956800-100966200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr6:100957400-100992400	Weak transcription	Small Intestine	intestine
27	chr6:100957800-100964800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:100958000-100964800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:100958200-100976600	Weak transcription	NHDF-Ad	bronchial
30	chr6:100958600-100974000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:100958800-100964400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:100959800-100964800	Weak transcription	Fetal Intestine Small	intestine
33	chr6:100959800-100966800	Weak transcription	Fetal Stomach	stomach
34	chr6:100960200-100966200	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:100960200-100978000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:100960600-100964800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:100960600-100967400	Weak transcription	Fetal Thymus	thymus
38	chr6:100960600-100973800	Weak transcription	HUVEC	blood vessel
39	chr6:100960600-100990200	Weak transcription	Brain Substantia Nigra	brain
40	chr6:100960800-100964600	Weak transcription	Fetal Intestine Large	intestine
41	chr6:100960800-100964600	Weak transcription	Lung	lung
42	chr6:100960800-100964800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:100960800-100965000	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:100960800-100965600	Weak transcription	Brain Anterior Caudate	brain
45	chr6:100960800-100965600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:100960800-100966000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:100960800-100966200	Weak transcription	Liver	Liver
48	chr6:100960800-100966400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:100960800-100966600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:100960800-100966800	Weak transcription	Fetal Lung	lung

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