Variant report

Variant	rs28417568
Chromosome Location	chr3:98526864-98526865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:98523635-98529478	U87	brain:	n/a	n/a
2	POLR2A	chr3:98523592-98529440	U87	brain:	n/a	n/a
3	POLR2A	chr3:98523586-98529440	U87	brain:	n/a	n/a
4	GATA3	chr3:98526787-98526984	SH-SY5Y	brain:	n/a	n/a
5	POLR2A	chr3:98523621-98529478	U87	brain:	n/a	n/a
6	POLR2A	chr3:98526798-98527085	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98310981..98313806-chr3:98526146..98529080,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-26P	TF binding region
ENSG00000080819	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10084679	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330381	0.85[AMR][1000 genomes]
rs13317610	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13318960	0.85[AMR][1000 genomes]
rs13320266	0.88[ASN][1000 genomes]
rs13320890	0.94[EUR][1000 genomes]
rs13322253	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28429424	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28489284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528154	0.85[AMR][1000 genomes]
rs28650813	0.85[AMR][1000 genomes]
rs3796133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56172805	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56857413	0.82[ASN][1000 genomes]
rs57962467	0.82[ASN][1000 genomes]
rs59906228	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72932691	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72932700	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934623	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72938577	0.82[ASN][1000 genomes]
rs9289699	0.85[AMR][1000 genomes]
rs9289700	0.85[AMR][1000 genomes]
rs9810407	0.88[ASN][1000 genomes]
rs9812438	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818215	0.88[ASN][1000 genomes]
rs9833945	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9836437	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9836915	0.88[ASN][1000 genomes]
rs9838166	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9838238	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9838706	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839559	1.00[EUR][1000 genomes]
rs9848335	0.85[AMR][1000 genomes]
rs9848583	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9862660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870500	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870940	0.85[AMR][1000 genomes]
rs9879302	0.85[AMR][1000 genomes]
rs9883751	0.81[AFR][1000 genomes];0.88[ASN][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	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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98503400-98576400	Weak transcription	Gastric	stomach
3	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
4	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
7	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
8	chr3:98516800-98528600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
10	chr3:98517200-98531400	Weak transcription	Hela-S3	cervix
11	chr3:98520600-98528200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:98522400-98533800	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr3:98523400-98531400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:98523600-98527000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:98523600-98527000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:98523600-98527000	Strong transcription	Adipose Nuclei	Adipose
17	chr3:98523600-98527200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:98523600-98527400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:98523600-98528200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:98523600-98528600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:98523600-98533800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:98523600-98535200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:98523800-98527000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:98523800-98527000	Strong transcription	Liver	Liver
25	chr3:98523800-98527000	Strong transcription	Pancreas	Pancrea
26	chr3:98523800-98527000	Strong transcription	Stomach Smooth Muscle	stomach
27	chr3:98523800-98527000	Strong transcription	K562	blood
28	chr3:98523800-98527200	Strong transcription	Brain Germinal Matrix	brain
29	chr3:98523800-98527200	Strong transcription	Ovary	ovary
30	chr3:98523800-98527400	Strong transcription	Fetal Kidney	kidney
31	chr3:98523800-98528200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:98523800-98528200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:98523800-98528200	Strong transcription	Fetal Intestine Large	intestine
34	chr3:98523800-98528200	Strong transcription	Left Ventricle	heart
35	chr3:98523800-98528400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:98523800-98528400	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:98523800-98529200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:98523800-98529200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:98523800-98529200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:98523800-98529400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:98523800-98529400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:98523800-98529600	Strong transcription	Fetal Lung	lung
43	chr3:98523800-98530000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:98523800-98530200	Strong transcription	Dnd41	blood
45	chr3:98523800-98530400	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr3:98523800-98530400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:98523800-98530600	Strong transcription	HUVEC	blood vessel
48	chr3:98523800-98531400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:98523800-98531400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:98523800-98533600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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