Variant report

Variant	rs2311801
Chromosome Location	chr3:49568095-49568096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49567639..49569337-chr3:49570059..49572705,2	MCF-7	breast:
2	chr3:49567781..49571690-chr3:49573086..49576036,4	K562	blood:
3	chr3:49567274..49570195-chr3:49712184..49713980,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11130197	0.91[YRI][hapmap]
rs11130201	0.97[AFR][1000 genomes]
rs11708174	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs11717485	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1996874	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3870334	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	0.82[ASW][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs4452334	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	0.86[AFR][1000 genomes]
rs4855872	1.00[EUR][1000 genomes]
rs4855874	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[EUR][1000 genomes]
rs4855878	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs55808753	0.86[AFR][1000 genomes]
rs55990645	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	1.00[EUR][1000 genomes]
rs56897974	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60011446	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.84[AFR][1000 genomes]
rs6446270	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs6446279	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.89[AFR][1000 genomes]
rs6446281	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762593	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs6766297	1.00[EUR][1000 genomes]
rs6787665	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	0.87[YRI][hapmap]
rs73830703	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831438	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831442	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834006	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7646393	0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	0.86[AFR][1000 genomes]
rs9830627	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49529600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr3:49539600-49568600	Weak transcription	Small Intestine	intestine
3	chr3:49546200-49577000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:49547000-49572000	Weak transcription	Fetal Brain Male	brain
5	chr3:49548400-49577400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:49549200-49568800	Weak transcription	Osteobl	bone
7	chr3:49550800-49568400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:49551400-49571400	Weak transcription	Stomach Mucosa	stomach
9	chr3:49551400-49572200	Weak transcription	NH-A	brain
10	chr3:49551600-49569400	Weak transcription	Fetal Kidney	kidney
11	chr3:49553800-49568400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:49554400-49568200	Weak transcription	NHDF-Ad	bronchial
13	chr3:49555400-49568200	Weak transcription	NHLF	lung
14	chr3:49555400-49568600	Weak transcription	Fetal Lung	lung
15	chr3:49555800-49568400	Weak transcription	HUVEC	blood vessel
16	chr3:49555800-49572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:49556000-49568600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:49557000-49568400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:49557200-49568200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:49557600-49572000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:49558000-49568200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:49558000-49568200	Weak transcription	Ovary	ovary
23	chr3:49558400-49568200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:49558400-49568200	Weak transcription	Brain Anterior Caudate	brain
25	chr3:49560600-49572600	Weak transcription	Psoas Muscle	Psoas
26	chr3:49561800-49568200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:49561800-49568200	Weak transcription	Lung	lung
28	chr3:49562000-49568200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:49562000-49568200	Weak transcription	Brain Substantia Nigra	brain
30	chr3:49562200-49568400	Weak transcription	Esophagus	oesophagus
31	chr3:49562400-49568200	Weak transcription	Right Ventricle	heart
32	chr3:49562600-49568200	Weak transcription	Brain Germinal Matrix	brain
33	chr3:49562600-49568200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:49562800-49568200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:49563000-49568200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:49563200-49569000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:49564000-49568400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:49565400-49572400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:49566200-49568400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:49566200-49568800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr3:49566600-49571400	Strong transcription	Primary T cells from cord blood	blood
42	chr3:49566800-49570200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:49566800-49570800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:49566800-49571800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:49566800-49572800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:49567000-49568200	Enhancers	Placenta	Placenta
47	chr3:49567000-49568400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:49567000-49569000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr3:49567000-49570200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:49567000-49570600	Strong transcription	A549	lung

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