Variant report

Variant	rs550016051
Chromosome Location	chr3:50226448-50226449
allele	A/G
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	SMC3	chr3:50226404-50227691	SK-N-SH	brain:	n/a	chr3:50226912-50226926 chr3:50226566-50226576
2	CTCF	chr3:50226403-50227243	HCT-116	colon:	n/a	chr3:50226911-50226927 chr3:50226910-50226928 chr3:50226912-50226925 chr3:50226905-50226926
3	POLR2A	chr3:50226208-50226551	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:50226117-50227882	PANC-1	pancreas:	n/a	n/a
5	RAD21	chr3:50226353-50227415	SK-N-SH	brain:	n/a	chr3:50226908-50226927
6	POLR2A	chr3:50225743-50227672	NB4	blood:	n/a	n/a
7	RAD21	chr3:50226419-50227334	HCT-116	colon:	n/a	chr3:50226908-50226927

No.	Distal block	Cell Line	Cell type
1	chr3:50158714..50160101-chr3:50225873..50227682,16	MCF-7	breast:
2	chr3:50158552..50159685-chr3:50226139..50227732,7	K562	blood:
3	chr3:50225100..50230290-chr3:50272107..50276590,4	MCF-7	breast:
4	chr3:50191309..50193703-chr3:50225240..50227025,2	MCF-7	breast:
5	chr3:50164397..50164965-chr3:50226441..50226966,2	K562	blood:
6	chr3:50192280..50192998-chr3:50226444..50226959,2	MCF-7	breast:
7	chr3:50219040..50221554-chr3:50225247..50227656,2	MCF-7	breast:
8	chr3:50193362..50195902-chr3:50224405..50227347,2	K562	blood:
9	chr3:50157801..50161419-chr3:50224013..50228566,6	MCF-7	breast:
10	chr3:50226233..50229498-chr3:50242660..50245494,3	K562	blood:
11	chr3:50224996..50226942-chr3:50236874..50238990,2	K562	blood:

Variant related genes	Relation type
GNAT1	TF binding region
ENSG00000114353	Chromatin interaction
ENSG00000001617	Chromatin interaction
ENSG00000188338	Chromatin interaction
ENSG00000235016	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
3	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
4	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	nsv876771	chr3:50225568-50247824	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50204600-50226600	Weak transcription	Brain Anterior Caudate	brain
2	chr3:50205400-50226600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:50205400-50226600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:50206400-50226600	Weak transcription	NHLF	lung
5	chr3:50208800-50226600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:50208800-50226600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:50208800-50226600	Weak transcription	Osteobl	bone
8	chr3:50210400-50229200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:50210400-50242400	Weak transcription	Right Atrium	heart
10	chr3:50210600-50229400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:50211400-50230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:50212200-50226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:50214200-50230600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:50215000-50226600	Weak transcription	HSMMtube	muscle
15	chr3:50218000-50228600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:50219400-50226600	Strong transcription	HMEC	breast
17	chr3:50220000-50231800	Weak transcription	K562	blood
18	chr3:50220200-50228400	Weak transcription	HUVEC	blood vessel
19	chr3:50220400-50228400	Weak transcription	Hela-S3	cervix
20	chr3:50220600-50226600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:50220800-50230200	Weak transcription	Colonic Mucosa	Colon
22	chr3:50221600-50228400	Weak transcription	HepG2	liver
23	chr3:50222400-50227400	Weak transcription	Aorta	Aorta
24	chr3:50223200-50226800	Weak transcription	Liver	Liver
25	chr3:50223200-50228400	Weak transcription	Fetal Kidney	kidney
26	chr3:50224000-50226600	Weak transcription	Right Ventricle	heart
27	chr3:50224200-50228800	Weak transcription	Fetal Intestine Small	intestine
28	chr3:50224200-50229800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:50224400-50231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:50224600-50230000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:50224800-50226600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:50224800-50226600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:50225000-50227800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:50225200-50227800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:50225200-50229400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:50225200-50230600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:50225400-50226600	Weak transcription	Fetal Lung	lung
38	chr3:50225400-50228600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:50225400-50230000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:50225600-50230000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:50225800-50232200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:50226000-50226600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:50226000-50226600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:50226000-50226800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:50226000-50227200	Weak transcription	Spleen	Spleen
46	chr3:50226000-50227200	Weak transcription	NHEK	skin
47	chr3:50226000-50230600	Weak transcription	Lung	lung
48	chr3:50226000-50231400	Weak transcription	Gastric	stomach
49	chr3:50226200-50226600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:50226200-50226600	Weak transcription	Brain Germinal Matrix	brain

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