Variant report

Variant	rs2624841
Chromosome Location	chr3:50198415-50198416
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	POLR2A	chr3:50198188-50198415	Hela-S3	cervix:	n/a	n/a
2	TCF7L2	chr3:50198095-50198498	Hela-S3	cervix:	n/a	n/a
3	ZBTB7A	chr3:50198207-50199182	ECC-1	luminal epithelium:	n/a	n/a
4	GATA2	chr3:50197954-50198499	HUVEC	blood vessel:	n/a	chr3:50198284-50198298
5	STAT3	chr3:50198378-50198467	MCF10A-Er-Src	breast:	n/a	chr3:50198409-50198421
6	STAT3	chr3:50198180-50198503	MCF10A-Er-Src	breast:	n/a	chr3:50198409-50198421 chr3:50198249-50198261 chr3:50198337-50198348
7	RFX5	chr3:50198208-50199132	Hela-S3	cervix:	n/a	n/a
8	BRCA1	chr3:50198168-50198507	Hela-S3	cervix:	n/a	n/a
9	SMC3	chr3:50197891-50198467	Hela-S3	cervix:	n/a	chr3:50198314-50198324
10	TCF12	chr3:50198261-50199219	ECC-1	luminal epithelium:	n/a	n/a
11	TBP	chr3:50198020-50198415	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:50197876-50198923	HUVEC	blood vessel:	n/a	n/a
13	RCOR1	chr3:50197794-50198431	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr3:50198057-50198475	K562	blood:	n/a	n/a
15	POLR2A	chr3:50198174-50199212	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50190470..50194491-chr3:50196225..50201802,7	K562	blood:
2	chr3:50197953..50200142-chr3:50211496..50213550,2	K562	blood:
3	chr3:50198100..50200142-chr3:50211400..50213550,2	K562	blood:
4	chr3:50191401..50200098-chr3:50206213..50213809,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235016	TF binding region
ENSG00000235016	Chromatin interaction
ENSG00000001617	Chromatin interaction
ENSG00000207922	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1046956	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919418	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12632110	0.91[EUR][1000 genomes]
rs12637671	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13059311	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064381	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067082	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13095697	1.00[ASN][1000 genomes]
rs13097720	1.00[ASN][1000 genomes]
rs14321	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17225749	1.00[ASN][1000 genomes]
rs17304079	1.00[ASN][1000 genomes]
rs2014004	1.00[ASN][1000 genomes]
rs2188151	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2236940	0.82[EUR][1000 genomes]
rs2236941	0.82[EUR][1000 genomes]
rs2518795	0.87[AMR][1000 genomes]
rs2518796	0.88[AMR][1000 genomes]
rs2526384	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526387	1.00[ASN][1000 genomes]
rs2526397	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526398	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624833	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624835	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2624838	0.92[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35137368	0.86[EUR][1000 genomes]
rs35219849	0.86[EUR][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs55924524	1.00[ASN][1000 genomes]
rs58648044	0.82[EUR][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62263602	1.00[ASN][1000 genomes]
rs6787892	1.00[ASN][1000 genomes]
rs6800021	0.80[AMR][1000 genomes]
rs6807194	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs71326915	1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7648652	1.00[ASN][1000 genomes]
rs9858297	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2624841	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624841	RBM6	cis	Artery Tibial	GTEx
rs2624841	HYAL3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50194200-50203800	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr3:50194200-50208800	Weak transcription	Pancreas	Pancrea
3	chr3:50194400-50199000	Enhancers	Stomach Mucosa	stomach
4	chr3:50194400-50201000	Weak transcription	Psoas Muscle	Psoas
5	chr3:50194600-50199000	Enhancers	Fetal Brain Male	brain
6	chr3:50194800-50200800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:50194800-50200800	Enhancers	Colon Smooth Muscle	Colon
8	chr3:50194800-50200800	Weak transcription	NHDF-Ad	bronchial
9	chr3:50194800-50202600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:50194800-50207600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr3:50195000-50201200	Enhancers	Adipose Nuclei	Adipose
12	chr3:50195200-50199000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:50195400-50210200	Genic enhancers	Fetal Stomach	stomach
14	chr3:50195400-50210600	Enhancers	Left Ventricle	heart
15	chr3:50195400-50210800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:50195600-50198800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:50195600-50200400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:50195800-50201000	Weak transcription	Thymus	Thymus
19	chr3:50196000-50200800	Weak transcription	HSMM	muscle
20	chr3:50196200-50199200	Genic enhancers	Placenta	Placenta
21	chr3:50196200-50199400	Enhancers	Fetal Muscle Trunk	muscle
22	chr3:50196200-50199600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:50196200-50211600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr3:50196400-50198600	Weak transcription	Osteobl	bone
25	chr3:50196400-50199600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:50196400-50200800	Weak transcription	Aorta	Aorta
27	chr3:50196400-50202200	Genic enhancers	Fetal Lung	lung
28	chr3:50196600-50198800	Weak transcription	Right Atrium	heart
29	chr3:50196600-50199200	Weak transcription	HepG2	liver
30	chr3:50196600-50199800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:50196600-50201000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:50196600-50201800	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:50196800-50198800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:50196800-50201200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:50196800-50202000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:50196800-50202000	Enhancers	Duodenum Mucosa	Duodenum
37	chr3:50196800-50202400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:50197000-50199000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:50197000-50199800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:50197000-50201000	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr3:50197000-50201000	Genic enhancers	HMEC	breast
42	chr3:50197000-50201400	Weak transcription	Fetal Thymus	thymus
43	chr3:50197000-50202200	Genic enhancers	Lung	lung
44	chr3:50197200-50199600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:50197200-50199600	Strong transcription	Brain Germinal Matrix	brain
46	chr3:50197200-50199800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr3:50197200-50200200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:50197200-50201000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:50197200-50211600	Genic enhancers	Esophagus	oesophagus
50	chr3:50197400-50199600	Strong transcription	Fetal Brain Female	brain

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