Variant report

Variant	rs9390171
Chromosome Location	chr6:144882961-144882962
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	chr6:144415654..144418323-chr6:144881509..144883316,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169976	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10499231	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1358433	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2091485	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2876586	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3793134	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3793135	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812245	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3812246	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4499947	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4896729	0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6570637	0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6915747	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7749805	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7749957	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7754789	0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7767389	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7770106	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7770800	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9376822	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs9390173	0.92[EUR][1000 genomes]
rs9399478	0.89[EUR][1000 genomes]
rs9399479	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9496995	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9497006	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs951571	0.89[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	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144807400-144904000	Weak transcription	Brain Substantia Nigra	brain
2	chr6:144850400-144903200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:144850400-144903200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:144850400-144904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:144853600-144896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:144857200-144904000	Weak transcription	Psoas Muscle	Psoas
7	chr6:144858200-144887800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr6:144861200-144885000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:144864800-144885200	Weak transcription	Colonic Mucosa	Colon
10	chr6:144864800-144885800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr6:144864800-144899000	Weak transcription	Small Intestine	intestine
12	chr6:144867400-144903800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:144869600-144887000	Strong transcription	Primary hematopoietic stem cells	blood
14	chr6:144869800-144885600	Strong transcription	Adipose Nuclei	Adipose
15	chr6:144870800-144898400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:144872000-144903000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:144873000-144903200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:144873000-144903800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:144874000-144904200	Weak transcription	Placenta	Placenta
20	chr6:144877000-144895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:144877000-144898000	Weak transcription	Right Ventricle	heart
22	chr6:144877000-144898200	Weak transcription	Fetal Intestine Small	intestine
23	chr6:144877000-144903000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:144877000-144904200	Weak transcription	Fetal Stomach	stomach
25	chr6:144878000-144903400	Weak transcription	Fetal Brain Male	brain
26	chr6:144878400-144898000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:144878400-144899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:144878600-144883400	Weak transcription	Ovary	ovary
29	chr6:144878600-144883400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:144878600-144898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:144878600-144898200	Weak transcription	Lung	lung
32	chr6:144878600-144901200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:144878800-144898000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:144879000-144883400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:144879000-144883400	Weak transcription	Left Ventricle	heart
36	chr6:144879000-144890400	Weak transcription	Liver	Liver
37	chr6:144879000-144890800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr6:144879000-144890800	Weak transcription	Pancreas	Pancrea
39	chr6:144879000-144898000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:144879000-144898200	Weak transcription	Esophagus	oesophagus
41	chr6:144879000-144898200	Weak transcription	Fetal Intestine Large	intestine
42	chr6:144879000-144898200	Weak transcription	Spleen	Spleen
43	chr6:144879000-144898200	Weak transcription	GM12878-XiMat	blood
44	chr6:144879200-144898800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:144879200-144899800	Weak transcription	NHLF	lung
46	chr6:144879200-144904000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:144879600-144883400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:144879600-144885600	Weak transcription	Fetal Kidney	kidney
49	chr6:144879600-144898000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr6:144879600-144898200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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