Variant report

Variant	rs9478790
Chromosome Location	chr6:151035340-151035341
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	chr6:151029067..151031162-chr6:151034859..151036741,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12664155	1.00[CEU][hapmap]
rs17080212	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs17080238	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs1968998	0.86[AMR][1000 genomes]
rs1968999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2279628	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3734411	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs4869689	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4869693	0.86[AMR][1000 genomes]
rs4869932	0.85[CEU][hapmap]
rs4869934	0.85[EUR][1000 genomes]
rs4869935	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4869936	0.85[EUR][1000 genomes]
rs4869938	0.85[EUR][1000 genomes]
rs4869939	0.85[EUR][1000 genomes]
rs5029652	0.85[EUR][1000 genomes]
rs6902743	0.85[EUR][1000 genomes]
rs72570328	0.84[AMR][1000 genomes]
rs72570331	0.84[AMR][1000 genomes]
rs72570332	0.84[AMR][1000 genomes]
rs72570334	0.84[AMR][1000 genomes]
rs72570350	0.82[AMR][1000 genomes]
rs7748886	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7772795	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9478786	0.85[EUR][1000 genomes]
rs9478787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9478791	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9480540	0.85[EUR][1000 genomes]
rs9480548	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9480549	0.85[EUR][1000 genomes]
rs9480550	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9480551	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9986516	0.85[EUR][1000 genomes]
rs9986520	0.85[EUR][1000 genomes]
rs9986597	0.83[EUR][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	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3439835	chr6:151027582-151036981	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1019919	chr6:151028969-151161789	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv538474	chr6:151028969-151161789	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:151021600-151040600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:151026800-151043600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:151029400-151041800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:151032200-151037600	Weak transcription	Gastric	stomach
5	chr6:151032800-151036600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:151033000-151035600	Enhancers	Fetal Lung	lung
7	chr6:151033000-151035800	Enhancers	Brain Substantia Nigra	brain
8	chr6:151033000-151035800	Enhancers	Fetal Heart	heart
9	chr6:151033000-151036200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:151033200-151035400	Enhancers	Right Atrium	heart
11	chr6:151033200-151035800	Enhancers	Fetal Kidney	kidney
12	chr6:151033200-151036000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:151033200-151036000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:151033200-151036000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:151033200-151036200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:151033400-151038000	Weak transcription	Esophagus	oesophagus
17	chr6:151033600-151035400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:151033600-151035600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:151033600-151037600	Weak transcription	Pancreas	Pancrea
20	chr6:151033600-151038000	Weak transcription	Primary B cells from cord blood	blood
21	chr6:151033600-151038200	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:151033600-151040200	Weak transcription	Fetal Stomach	stomach
23	chr6:151033600-151042000	Weak transcription	Fetal Intestine Small	intestine
24	chr6:151033600-151050200	Weak transcription	Lung	lung
25	chr6:151033800-151035400	Enhancers	Placenta	Placenta
26	chr6:151034000-151035400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr6:151034000-151035600	Enhancers	Brain Hippocampus Middle	brain
28	chr6:151034000-151040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:151034200-151035800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:151034200-151037600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:151034200-151037600	Weak transcription	Small Intestine	intestine
32	chr6:151034200-151038400	Weak transcription	Stomach Mucosa	stomach
33	chr6:151034200-151038600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:151034200-151040600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:151034200-151041800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:151034200-151042000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:151034400-151038000	Weak transcription	Thymus	Thymus
38	chr6:151034400-151041000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:151034400-151041200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:151034400-151042000	Weak transcription	Brain Germinal Matrix	brain
41	chr6:151034600-151035800	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:151034800-151036000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:151034800-151040600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:151034800-151040800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:151034800-151040800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:151035000-151038000	Weak transcription	Left Ventricle	heart
47	chr6:151035000-151038400	Weak transcription	Fetal Thymus	thymus
48	chr6:151035000-151040200	Weak transcription	Spleen	Spleen
49	chr6:151035000-151040800	Weak transcription	Fetal Brain Female	brain
50	chr6:151035000-151066400	Weak transcription	Right Ventricle	heart

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