Variant report

Variant	rs9843055
Chromosome Location	chr3:52459323-52459324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52458604..52461209-chr3:52511392..52513650,2	MCF-7	breast:
2	chr3:52456788..52463599-chr3:52473182..52477176,6	K562	blood:
3	chr3:52456149..52459336-chr3:52479539..52482914,3	MCF-7	breast:
4	chr3:52457971..52460550-chr3:52489642..52491148,2	K562	blood:
5	chr3:52452552..52454211-chr3:52457966..52459980,2	K562	blood:
6	chr3:52445862..52449663-chr3:52459054..52463176,4	K562	blood:
7	chr3:52458322..52461019-chr3:52473695..52476448,2	K562	blood:
8	chr3:52455484..52457043-chr3:52458911..52460495,2	K562	blood:
9	chr3:52445430..52449700-chr3:52458651..52461042,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000010322	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10212560	1.00[EUR][1000 genomes]
rs10440116	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10510759	1.00[MEX][hapmap]
rs10865972	1.00[YRI][hapmap]
rs13318570	1.00[AMR][1000 genomes]
rs1541495	1.00[YRI][hapmap]
rs17052143	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28413740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687614	1.00[YRI][hapmap]
rs5743834	1.00[EUR][1000 genomes]
rs9813448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813489	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[EUR][1000 genomes]
rs9813653	0.91[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814016	1.00[EUR][1000 genomes]
rs9815559	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821916	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9824342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834363	1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834919	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9836166	1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842960	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9844178	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9864989	1.00[EUR][1000 genomes]
rs9868332	1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52445600-52471600	Weak transcription	Gastric	stomach
2	chr3:52446200-52463000	Weak transcription	Lung	lung
3	chr3:52446200-52465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:52446200-52467800	Weak transcription	Esophagus	oesophagus
5	chr3:52446400-52470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:52446800-52460000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:52446800-52462400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:52446800-52463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:52446800-52466000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:52447000-52462800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:52447000-52464000	Weak transcription	Osteobl	bone
12	chr3:52447000-52470200	Weak transcription	Fetal Lung	lung
13	chr3:52447200-52461400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:52447200-52462400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:52447200-52462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:52447200-52462800	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:52447200-52463000	Weak transcription	Left Ventricle	heart
18	chr3:52447200-52463000	Weak transcription	Right Ventricle	heart
19	chr3:52447200-52468000	Weak transcription	Colonic Mucosa	Colon
20	chr3:52447400-52462800	Weak transcription	Brain Angular Gyrus	brain
21	chr3:52447400-52466200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:52447400-52467600	Weak transcription	NHEK	skin
23	chr3:52448200-52463000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:52448600-52471200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:52450200-52478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:52454200-52467600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:52454400-52462800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:52455000-52462800	Weak transcription	Liver	Liver
29	chr3:52455000-52462800	Weak transcription	Placenta	Placenta
30	chr3:52455000-52463400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:52455000-52466000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:52455200-52462800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:52455200-52463600	Weak transcription	Fetal Intestine Small	intestine
34	chr3:52455200-52464000	Weak transcription	Fetal Intestine Large	intestine
35	chr3:52455200-52465800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:52455400-52462800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:52455400-52463000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:52455400-52466000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr3:52456200-52467000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:52456400-52459800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:52456400-52462800	Weak transcription	Brain Substantia Nigra	brain
42	chr3:52456400-52463000	Weak transcription	Right Atrium	heart
43	chr3:52456800-52462400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:52457000-52462800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:52457200-52462600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:52457200-52466400	Weak transcription	Spleen	Spleen
47	chr3:52457400-52462800	Weak transcription	Fetal Stomach	stomach
48	chr3:52457600-52462800	Weak transcription	Adipose Nuclei	Adipose
49	chr3:52457600-52462800	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:52457800-52463000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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