Variant report

Variant	rs9846534
Chromosome Location	chr3:105581750-105581751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:105580037..105582399-chr3:105585433..105589052,3	MCF-7	breast:
2	chr3:105579577..105582453-chr3:105582537..105585477,2	MCF-7	breast:
3	chr3:105578910..105582345-chr3:105586229..105588462,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1021858	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1021859	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1039544	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10511246	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075739	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11921710	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11924742	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12633654	0.84[ASN][1000 genomes]
rs12633854	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12635232	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12637560	0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs12637809	0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12639271	0.81[ASN][1000 genomes]
rs1503921	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1561922	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs16851523	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs16851539	0.92[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs16851563	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs16851570	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs16851587	0.88[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs16851630	0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1867192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867195	0.81[CEU][hapmap]
rs1910499	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1947000	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2089091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197208	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2197209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3996189	0.88[CEU][hapmap]
rs4447799	0.86[CEU][hapmap]
rs4894840	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4894957	0.88[CEU][hapmap]
rs57520912	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58340800	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59534462	0.89[ASN][1000 genomes]
rs59611997	0.84[ASN][1000 genomes]
rs60619938	0.82[ASN][1000 genomes]
rs6437620	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437621	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437624	0.87[CEU][hapmap]
rs6437626	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6767627	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6788366	0.88[CEU][hapmap]
rs6804152	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6807382	0.88[CEU][hapmap]
rs73854891	0.85[ASN][1000 genomes]
rs73854894	0.89[ASN][1000 genomes]
rs73857222	0.88[ASN][1000 genomes]
rs7619449	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7624400	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7629357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634844	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7641825	0.93[CEU][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes]
rs7648842	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649466	0.93[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7651784	0.87[CEU][hapmap]
rs9631436	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9657904	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9789988	0.82[ASN][1000 genomes]
rs9826886	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841500	0.87[CEU][hapmap]
rs9869648	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9874600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
3	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:105562000-105586000	Weak transcription	K562	blood
7	chr3:105563000-105584600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:105563400-105583000	Weak transcription	Spleen	Spleen
10	chr3:105563800-105584400	Weak transcription	Brain Angular Gyrus	brain
11	chr3:105564800-105585000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:105565600-105584800	Weak transcription	NHEK	skin
13	chr3:105566200-105584800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:105566200-105585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:105566600-105584600	Weak transcription	Fetal Stomach	stomach
16	chr3:105567000-105583000	Weak transcription	Brain Substantia Nigra	brain
17	chr3:105567000-105584200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:105567200-105583200	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:105567200-105584000	Weak transcription	Brain Anterior Caudate	brain
20	chr3:105567200-105584600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
23	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
24	chr3:105569400-105584000	Weak transcription	A549	lung
25	chr3:105569800-105586200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:105570200-105584200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:105570600-105584200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:105571000-105582200	Weak transcription	Brain Germinal Matrix	brain
29	chr3:105571200-105584600	Weak transcription	NHLF	lung
30	chr3:105572000-105586200	Weak transcription	Lung	lung
31	chr3:105572200-105584200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:105572200-105584600	Weak transcription	HSMMtube	muscle
33	chr3:105572200-105585000	Weak transcription	Thymus	Thymus
34	chr3:105572200-105585400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:105572400-105582800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:105572400-105583000	Weak transcription	HMEC	breast
37	chr3:105572600-105582800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:105572600-105582800	Weak transcription	Dnd41	blood
39	chr3:105572600-105585200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:105572600-105585800	Weak transcription	Fetal Thymus	thymus
41	chr3:105572800-105585800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:105573200-105585000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:105573400-105584200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:105573800-105583000	Weak transcription	Fetal Intestine Small	intestine
45	chr3:105577000-105582200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:105577000-105582800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:105577000-105583000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:105577000-105584000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:105577200-105582600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:105577400-105582400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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