Variant report

Variant	rs17321330
Chromosome Location	chr3:113010303-113010304
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	chr3:113005964..113007970-chr3:113009934..113012808,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10934228	0.85[ASW][hapmap];0.87[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.81[TSI][hapmap]
rs11715198	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs12488964	0.88[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs1979554	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2054823	0.88[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs2171293	0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs2895413	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682138	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs6438140	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6438143	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs6438144	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs6438147	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs66524865	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768117	0.89[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs6775574	0.88[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs6777880	0.84[AMR][1000 genomes]
rs7618884	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7623122	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs7625841	0.88[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs7633428	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7650538	0.88[CEU][hapmap]
rs775232	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs775233	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9682734	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9848087	0.88[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs9866748	0.88[CEU][hapmap]
rs9869141	0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv521829	chr3:113007525-113010950	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17321330	SIDT1	cis	parietal	SCAN
rs17321330	WDR52	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
4	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
7	chr3:112995400-113035800	Weak transcription	Lung	lung
8	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
10	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
11	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
14	chr3:112998600-113036000	Weak transcription	Gastric	stomach
15	chr3:113000200-113016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:113000800-113014400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
19	chr3:113003200-113015400	Weak transcription	Brain Germinal Matrix	brain
20	chr3:113003400-113022600	Weak transcription	Colonic Mucosa	Colon
21	chr3:113003800-113016200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:113003800-113023000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:113004200-113023800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:113004600-113016200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:113005600-113029800	Weak transcription	Fetal Intestine Large	intestine
26	chr3:113006200-113010400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:113006200-113010400	Weak transcription	Ovary	ovary
28	chr3:113006200-113035400	Weak transcription	Esophagus	oesophagus
29	chr3:113006200-113036000	Weak transcription	Pancreas	Pancrea
30	chr3:113006600-113024000	Weak transcription	HSMMtube	muscle
31	chr3:113006800-113010800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:113006800-113015800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:113006800-113022600	Weak transcription	Hela-S3	cervix
34	chr3:113006800-113031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:113007000-113010600	Weak transcription	NHDF-Ad	bronchial
36	chr3:113007000-113012400	Weak transcription	A549	lung
37	chr3:113007000-113016400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:113007000-113022000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:113007000-113022600	Weak transcription	Liver	Liver
40	chr3:113007000-113022800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:113007000-113023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:113007000-113028000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:113007000-113034400	Weak transcription	HSMM	muscle
44	chr3:113007200-113043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:113007600-113010400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:113007600-113034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:113008000-113014000	Weak transcription	Primary T cells from cord blood	blood
48	chr3:113008000-113023600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:113008200-113035800	Weak transcription	Fetal Intestine Small	intestine
50	chr3:113008400-113023800	Weak transcription	Fetal Muscle Leg	muscle

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