Variant report

Variant	rs543953199
Chromosome Location	chr3:50226622-50226623
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	RAD21	chr3:50226597-50227231	A549	lung:	n/a	chr3:50226908-50226927
2	RAD21	chr3:50226531-50227191	HepG2	liver:	n/a	chr3:50226908-50226927
3	MYC	chr3:50226536-50227066	NB4	blood:	n/a	n/a
4	POLR2A	chr3:50226483-50227836	Hela-S3	cervix:	n/a	n/a
5	SMC3	chr3:50226404-50227691	SK-N-SH	brain:	n/a	chr3:50226912-50226926 chr3:50226566-50226576
6	POLR2A	chr3:50226454-50227504	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr3:50226572-50227244	HCT-116	colon:	n/a	chr3:50226911-50226927 chr3:50226910-50226928 chr3:50226912-50226925 chr3:50226905-50226926
8	POLR2A	chr3:50226563-50227977	MCF-7	breast:	n/a	n/a
9	HCFC1	chr3:50226516-50227512	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr3:50226403-50227243	HCT-116	colon:	n/a	chr3:50226911-50226927 chr3:50226910-50226928 chr3:50226912-50226925 chr3:50226905-50226926
11	RAD21	chr3:50226622-50227138	IMR90	lung:	n/a	chr3:50226908-50226927
12	POLR2A	chr3:50226530-50227634	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:50226117-50227882	PANC-1	pancreas:	n/a	n/a
14	RAD21	chr3:50226602-50227214	ECC-1	luminal epithelium:	n/a	chr3:50226908-50226927
15	POLR2A	chr3:50226564-50227087	HepG2	liver:	n/a	n/a
16	RAD21	chr3:50226353-50227415	SK-N-SH	brain:	n/a	chr3:50226908-50226927
17	CTCF	chr3:50226616-50227224	MCF-7	breast:	n/a	chr3:50226911-50226927 chr3:50226910-50226928 chr3:50226912-50226925 chr3:50226905-50226926
18	CTCF	chr3:50226531-50227222	SK-N-SH	brain:	n/a	chr3:50226911-50226927 chr3:50226910-50226928 chr3:50226912-50226925 chr3:50226905-50226926
19	POLR2A	chr3:50226612-50227296	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:50226564-50227965	HUVEC	blood vessel:	n/a	n/a
21	RAD21	chr3:50226579-50227078	SK-N-SH_RA	brain:	n/a	chr3:50226908-50226927
22	POLR2A	chr3:50225743-50227672	NB4	blood:	n/a	n/a
23	RAD21	chr3:50226537-50227323	HCT-116	colon:	n/a	chr3:50226908-50226927
24	POLR2A	chr3:50226587-50227835	PANC-1	pancreas:	n/a	n/a
25	RAD21	chr3:50226419-50227334	HCT-116	colon:	n/a	chr3:50226908-50226927
26	RAD21	chr3:50226487-50227260	ECC-1	luminal epithelium:	n/a	chr3:50226908-50226927
27	CTCF	chr3:50226601-50227108	A549	lung:	n/a	chr3:50226911-50226927 chr3:50226910-50226928 chr3:50226912-50226925 chr3:50226905-50226926
28	POLR2A	chr3:50226590-50227784	HUVEC	blood vessel:	n/a	n/a

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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50210400-50229200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:50210400-50242400	Weak transcription	Right Atrium	heart
3	chr3:50210600-50229400	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:50211400-50230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:50214200-50230600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:50218000-50228600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:50220000-50231800	Weak transcription	K562	blood
8	chr3:50220200-50228400	Weak transcription	HUVEC	blood vessel
9	chr3:50220400-50228400	Weak transcription	Hela-S3	cervix
10	chr3:50220800-50230200	Weak transcription	Colonic Mucosa	Colon
11	chr3:50221600-50228400	Weak transcription	HepG2	liver
12	chr3:50222400-50227400	Weak transcription	Aorta	Aorta
13	chr3:50223200-50226800	Weak transcription	Liver	Liver
14	chr3:50223200-50228400	Weak transcription	Fetal Kidney	kidney
15	chr3:50224200-50228800	Weak transcription	Fetal Intestine Small	intestine
16	chr3:50224200-50229800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:50224400-50231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:50224600-50230000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:50225000-50227800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:50225200-50227800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:50225200-50229400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:50225200-50230600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:50225400-50228600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:50225400-50230000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:50225600-50230000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:50225800-50232200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:50226000-50226800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:50226000-50227200	Weak transcription	Spleen	Spleen
29	chr3:50226000-50227200	Weak transcription	NHEK	skin
30	chr3:50226000-50230600	Weak transcription	Lung	lung
31	chr3:50226000-50231400	Weak transcription	Gastric	stomach
32	chr3:50226200-50226800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:50226200-50226800	Enhancers	Fetal Brain Female	brain
34	chr3:50226200-50226800	Enhancers	Stomach Mucosa	stomach
35	chr3:50226200-50227200	Enhancers	Fetal Muscle Leg	muscle
36	chr3:50226200-50227400	Enhancers	Fetal Brain Male	brain
37	chr3:50226200-50227600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:50226200-50229800	Weak transcription	Adipose Nuclei	Adipose
39	chr3:50226400-50226800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:50226400-50226800	Genic enhancers	Fetal Stomach	stomach
41	chr3:50226400-50227000	Genic enhancers	Placenta	Placenta
42	chr3:50226400-50227200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:50226400-50227200	Weak transcription	Esophagus	oesophagus
44	chr3:50226400-50227400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:50226400-50227400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr3:50226400-50228800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:50226400-50229400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:50226400-50232200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:50226600-50226800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr3:50226600-50226800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links