Variant report

Variant	rs7646393
Chromosome Location	chr3:49531041-49531042
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	chr3:49530765..49533090-chr3:49535053..49538549,4	K562	blood:
2	chr3:49506988..49509379-chr3:49529279..49532110,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11130197	1.00[YRI][hapmap]
rs11130201	0.94[AFR][1000 genomes]
rs11708174	1.00[YRI][hapmap]
rs11717485	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1996874	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3870334	0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4452334	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	0.94[AFR][1000 genomes]
rs4855872	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[EUR][1000 genomes]
rs4855878	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs55808753	0.94[AFR][1000 genomes]
rs55990645	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60011446	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.92[AFR][1000 genomes]
rs6446270	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs6446279	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.97[AFR][1000 genomes]
rs6446281	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.92[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[YRI][hapmap]
rs6766297	1.00[EUR][1000 genomes]
rs6787665	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	1.00[YRI][hapmap]
rs73830703	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.89[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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831440	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831441	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834006	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8179172	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	0.94[AFR][1000 genomes]
rs9830627	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9861805	1.00[EUR][1000 genomes]
rs9869504	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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:49510000-49535600	Weak transcription	NHLF	lung
5	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:49514400-49532400	Weak transcription	GM12878-XiMat	blood
7	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:49514800-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:49515000-49532800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:49515000-49535400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:49515200-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:49515200-49532400	Weak transcription	Colonic Mucosa	Colon
13	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
15	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
16	chr3:49516800-49532400	Weak transcription	Small Intestine	intestine
17	chr3:49516800-49534800	Weak transcription	Liver	Liver
18	chr3:49516800-49537600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:49517000-49547800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:49517200-49547800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:49519400-49535200	Weak transcription	K562	blood
22	chr3:49520400-49532800	Weak transcription	Primary B cells from cord blood	blood
23	chr3:49522200-49547800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:49522400-49537800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:49522400-49548000	Weak transcription	Spleen	Spleen
26	chr3:49522800-49531600	Weak transcription	Lung	lung
27	chr3:49523400-49531200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:49523400-49548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:49523400-49548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:49523600-49531200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:49523600-49535200	Weak transcription	Fetal Heart	heart
32	chr3:49523600-49535200	Weak transcription	A549	lung
33	chr3:49523600-49535400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:49523600-49536200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:49523600-49537000	Weak transcription	HMEC	breast
36	chr3:49523600-49537000	Weak transcription	HSMM	muscle
37	chr3:49523600-49537000	Weak transcription	NHDF-Ad	bronchial
38	chr3:49523600-49537600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:49523600-49548200	Weak transcription	Brain Substantia Nigra	brain
40	chr3:49524400-49532400	Strong transcription	Fetal Intestine Small	intestine
41	chr3:49524600-49536200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:49524800-49531200	Strong transcription	Fetal Muscle Leg	muscle
43	chr3:49525000-49534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:49526000-49547800	Weak transcription	Dnd41	blood
45	chr3:49526000-49548000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:49526200-49537000	Weak transcription	NHEK	skin
47	chr3:49526200-49537800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:49526800-49531200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:49527000-49532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:49527400-49532400	Weak transcription	Primary monocytes fromperipheralblood	blood

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