Variant report

Variant	rs278384
Chromosome Location	chr3:98514292-98514293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98504178..98506190-chr3:98512483..98514423,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383908	1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1600788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1818053	1.00[YRI][hapmap]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2173598	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2448985	1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470820	0.86[YRI][hapmap]
rs2470828	1.00[AMR][1000 genomes]
rs2470839	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	1.00[AMR][1000 genomes]
rs2470856	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278375	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4273318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	1.00[AMR][1000 genomes]
rs5013928	0.84[ASW][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs7373983	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7617405	1.00[CHD][hapmap]
rs7626395	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828611	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs828619	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][1000 genomes]
rs9883226	1.00[YRI][hapmap]
rs996199	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
10	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
11	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
12	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
14	chr3:98499800-98514800	Weak transcription	Dnd41	blood
15	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
16	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:98503400-98518200	Weak transcription	Ovary	ovary
19	chr3:98503400-98576400	Weak transcription	Gastric	stomach
20	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:98504600-98517000	Weak transcription	HSMMtube	muscle
22	chr3:98504600-98519400	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
24	chr3:98504800-98515000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:98504800-98517400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:98505000-98515200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:98505400-98515200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:98505400-98518400	Weak transcription	Fetal Thymus	thymus
30	chr3:98505400-98523800	Weak transcription	Pancreas	Pancrea
31	chr3:98505400-98524400	Weak transcription	Thymus	Thymus
32	chr3:98505800-98524600	Weak transcription	Psoas Muscle	Psoas
33	chr3:98506000-98515200	Weak transcription	Aorta	Aorta
34	chr3:98506200-98515000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:98506200-98515600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:98506200-98518000	Weak transcription	Fetal Intestine Large	intestine
37	chr3:98506400-98515600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:98506400-98516400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:98506400-98519400	Weak transcription	Brain Anterior Caudate	brain
40	chr3:98506400-98524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:98506600-98515400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:98506800-98523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:98507800-98514600	Strong transcription	Liver	Liver
44	chr3:98507800-98517400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:98507800-98517400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:98507800-98518200	Weak transcription	Right Ventricle	heart
47	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
48	chr3:98508000-98515000	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:98508000-98516600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:98508000-98519600	Weak transcription	Fetal Lung	lung

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