Variant report

Variant	rs61010376
Chromosome Location	chr3:99570825-99570826
allele	A/C
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	MAFK	chr3:99570770-99570970	HepG2	liver:	n/a	chr3:99570910-99570926
2	POLR2A	chr3:99570547-99571200	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:99569399-99571159	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99570458..99572667-chr3:99573247..99575806,2	MCF-7	breast:
2	chr3:99566203..99568540-chr3:99570392..99572106,2	MCF-7	breast:

Variant related genes	Relation type
FILIP1L	TF binding region
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1038295	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10804762	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485299	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12486901	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489030	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491153	0.84[EUR][1000 genomes]
rs12493124	0.93[EUR][1000 genomes]
rs1492343	0.83[ASN][1000 genomes]
rs1871847	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35590972	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928222	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55874130	0.93[EUR][1000 genomes]
rs55881709	0.89[EUR][1000 genomes]
rs55964918	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140081	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223679	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260910	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335268	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60119031	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6792339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800456	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73858966	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73859911	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73860464	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73860470	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7632345	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635633	0.89[EUR][1000 genomes]
rs7635871	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99557000-99573600	Weak transcription	Small Intestine	intestine
4	chr3:99559000-99578000	Weak transcription	HMEC	breast
5	chr3:99562200-99573200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:99562200-99578000	Weak transcription	NHEK	skin
7	chr3:99562600-99578200	Weak transcription	Fetal Kidney	kidney
8	chr3:99562800-99580200	Weak transcription	Gastric	stomach
9	chr3:99563000-99575000	Weak transcription	Placenta	Placenta
10	chr3:99563000-99577600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:99563200-99572200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:99563200-99574800	Weak transcription	Psoas Muscle	Psoas
13	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:99563800-99574800	Weak transcription	Pancreas	Pancrea
15	chr3:99564200-99577600	Weak transcription	Primary B cells from cord blood	blood
16	chr3:99565000-99572000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:99565400-99577600	Weak transcription	Fetal Heart	heart
19	chr3:99565600-99573600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:99565600-99573600	Weak transcription	Fetal Lung	lung
21	chr3:99565600-99574800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:99565600-99574800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:99565600-99589400	Weak transcription	K562	blood
25	chr3:99566000-99571800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:99566000-99571800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:99566000-99572000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:99566000-99573200	Weak transcription	Liver	Liver
29	chr3:99566000-99578400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:99567000-99571600	Strong transcription	NH-A	brain
31	chr3:99567200-99572000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:99567600-99573600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:99567600-99576200	Weak transcription	Stomach Mucosa	stomach
34	chr3:99567800-99571800	Weak transcription	Right Atrium	heart
35	chr3:99567800-99572800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:99567800-99573400	Strong transcription	HepG2	liver
37	chr3:99567800-99581600	Weak transcription	Spleen	Spleen
38	chr3:99568000-99571000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:99568000-99571000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr3:99568000-99578600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:99568000-99580000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:99568400-99572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:99568400-99575000	Weak transcription	GM12878-XiMat	blood
44	chr3:99568400-99576000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:99568600-99577600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:99568800-99574800	Weak transcription	NHDF-Ad	bronchial
47	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
48	chr3:99569400-99572200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:99569600-99571000	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:99569800-99571800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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