Variant report

Variant	rs41291724
Chromosome Location	chr3:50294066-50294067
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50294059-50294164	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:50293586-50295205	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:50293604-50294072	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:50293841-50294071	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:50293586-50295957	HL-60	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50291997..50295519-chr3:50296180..50299303,4	MCF-7	breast:
2	chr3:50293747..50295970-chr3:50606767..50608442,2	MCF-7	breast:
3	chr3:50283737..50287668-chr3:50290117..50294367,4	K562	blood:
4	chr3:50275833..50279919-chr3:50292841..50298987,5	MCF-7	breast:
5	chr3:50272477..50276068-chr3:50288828..50297512,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230454	TF binding region
ENSG00000114353	Chromatin interaction
ENSG00000213600	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000114735	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10510755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635953	0.81[ASN][1000 genomes]
rs2071802	0.89[ASN][1000 genomes]
rs2071803	0.92[ASN][1000 genomes]
rs2073498	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2097247	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236939	0.81[AMR][1000 genomes]
rs2301639	0.92[ASN][1000 genomes]
rs28365992	0.85[AMR][1000 genomes]
rs3755832	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806708	1.00[AMR][1000 genomes]
rs45536634	0.92[ASN][1000 genomes]
rs57319506	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57462170	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57842657	0.81[AMR][1000 genomes]
rs58051625	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60247651	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
7	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
11	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
12	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
19	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription 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 miRNA target site	53 gene(s)	inside rSNPs	diseases
20	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription 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	104 gene(s)	inside rSNPs	diseases
21	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
23	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
24	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
25	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
26	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
27	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
28	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50276400-50294400	Genic enhancers	Lung	lung
2	chr3:50284200-50297000	Genic enhancers	Fetal Muscle Trunk	muscle
3	chr3:50284400-50295000	Genic enhancers	Spleen	Spleen
4	chr3:50284400-50295800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:50284400-50297000	Genic enhancers	Fetal Muscle Leg	muscle
6	chr3:50284800-50300600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:50285200-50294400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:50285200-50296000	Strong transcription	Dnd41	blood
9	chr3:50285200-50296600	Strong transcription	Thymus	Thymus
10	chr3:50286000-50296200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:50286800-50297000	Weak transcription	A549	lung
12	chr3:50287200-50296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:50287400-50294400	Genic enhancers	Adipose Nuclei	Adipose
14	chr3:50287600-50295400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:50287800-50297200	Weak transcription	Small Intestine	intestine
16	chr3:50288200-50294800	Strong transcription	Fetal Intestine Large	intestine
17	chr3:50288200-50295600	Strong transcription	Fetal Thymus	thymus
18	chr3:50288600-50296200	Strong transcription	Primary T cells from cord blood	blood
19	chr3:50288600-50296600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:50288800-50295800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:50288800-50296000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:50289000-50296000	Strong transcription	Rectal Smooth Muscle	rectum
23	chr3:50289000-50296200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr3:50289000-50296200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:50289000-50296400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:50289000-50297000	Weak transcription	Fetal Heart	heart
27	chr3:50289000-50297000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr3:50289000-50297600	Genic enhancers	HUVEC	blood vessel
29	chr3:50289200-50296000	Strong transcription	Colonic Mucosa	Colon
30	chr3:50289400-50296000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:50289400-50297000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:50289400-50297000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:50289400-50297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:50289600-50295200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:50289600-50296200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:50289600-50296200	Strong transcription	Ovary	ovary
37	chr3:50289800-50296400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:50289800-50296600	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:50290000-50296800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:50290400-50295800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:50290600-50297000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:50291200-50295600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:50291200-50296200	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr3:50291600-50296000	Genic enhancers	Brain Anterior Caudate	brain
45	chr3:50291600-50296800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:50292000-50294200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:50292000-50295400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:50292400-50294200	Weak transcription	Fetal Brain Male	brain
49	chr3:50292400-50294200	Strong transcription	Right Ventricle	heart
50	chr3:50292400-50294400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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