Variant report

Variant	rs2624839
Chromosome Location	chr3:50202231-50202232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50201604..50203963-chr3:50205181..50207693,2	K562	blood:
2	chr3:50200763..50203311-chr3:50212854..50214994,2	MCF-7	breast:
3	chr3:50200976..50202928-chr3:50203961..50206728,2	MCF-7	breast:
4	chr3:50195147..50197422-chr3:50200868..50203043,2	K562	blood:
5	chr3:50175980..50179731-chr3:50201223..50204362,3	K562	blood:
6	chr3:50200725..50202849-chr3:50210057..50211879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207922	Chromatin interaction
ENSG00000001617	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1005678	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130248	0.84[CHD][hapmap]
rs12054052	0.84[ASN][1000 genomes]
rs12054403	0.84[CHD][hapmap]
rs12485909	0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs12487392	0.81[ASN][1000 genomes]
rs12488302	0.84[CHD][hapmap]
rs12492880	0.84[CHD][hapmap]
rs12494414	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs12632110	0.90[CHD][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12721544	0.83[ASN][1000 genomes]
rs2021734	0.85[ASN][1000 genomes]
rs2071203	0.84[CHD][hapmap]
rs2071204	0.84[CHD][hapmap]
rs2072053	0.87[ASN][1000 genomes]
rs2072054	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs2073500	0.84[CHD][hapmap]
rs2188151	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2233476	0.84[CHD][hapmap]
rs2236940	0.88[CHD][hapmap];0.80[MEX][hapmap]
rs2236941	0.88[CHD][hapmap];0.80[MEX][hapmap]
rs2236944	0.84[CHD][hapmap]
rs2236946	0.84[CHD][hapmap]
rs2285043	0.84[CHD][hapmap]
rs2298953	0.86[CHD][hapmap]
rs2298954	0.86[CHD][hapmap]
rs2518795	0.93[EUR][1000 genomes]
rs2518796	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.93[EUR][1000 genomes]
rs2526389	0.83[EUR][1000 genomes]
rs2624838	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3213621	0.84[CHD][hapmap]
rs35455589	0.82[CHD][hapmap]
rs35587949	0.84[CHD][hapmap]
rs3774739	0.93[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3774741	0.92[ASN][1000 genomes]
rs3774748	0.89[ASN][1000 genomes]
rs3774752	0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3774753	0.81[CHD][hapmap]
rs3774755	0.82[CHD][hapmap]
rs4688682	0.86[CHD][hapmap]
rs4688732	0.84[CHD][hapmap]
rs4688734	0.84[CHD][hapmap]
rs4688741	0.86[CHD][hapmap]
rs4688746	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4688747	0.92[ASN][1000 genomes]
rs58137261	0.83[ASN][1000 genomes]
rs58191283	0.83[ASN][1000 genomes]
rs6800021	0.92[EUR][1000 genomes]
rs7645537	0.86[CHD][hapmap]
rs9852677	0.83[CHD][hapmap]
rs9882618	0.80[ASN][1000 genomes]
rs9883222	0.86[CHD][hapmap]

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	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
26	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
27	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
28	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2624839	GNL3	cis	cerebellum	SCAN
rs2624839	PTH1R	cis	parietal	SCAN
rs2624839	GNL3	cis	parietal	SCAN
rs2624839	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624839	RNF123	cis	parietal	SCAN
rs2624839	RBM6	cis	parietal	SCAN
rs2624839	RBM6	cis	cerebellum	SCAN
rs2624839	RBM6	cis	Artery Tibial	GTEx

Chromatin state (count:94 , 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	chr3:50194800-50202600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:50194800-50207600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr3:50195400-50210200	Genic enhancers	Fetal Stomach	stomach
6	chr3:50195400-50210600	Enhancers	Left Ventricle	heart
7	chr3:50195400-50210800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:50196200-50211600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr3:50196800-50202400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:50197200-50211600	Genic enhancers	Esophagus	oesophagus
11	chr3:50197800-50202400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:50197800-50205800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr3:50197800-50207600	Enhancers	Colonic Mucosa	Colon
14	chr3:50198600-50206400	Enhancers	Gastric	stomach
15	chr3:50198800-50202800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:50198800-50202800	Enhancers	Right Atrium	heart
17	chr3:50199000-50202800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:50199000-50202800	Weak transcription	Fetal Heart	heart
19	chr3:50199000-50202800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:50199000-50203200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:50199200-50204600	Enhancers	Brain Anterior Caudate	brain
22	chr3:50199200-50205200	Enhancers	Stomach Mucosa	stomach
23	chr3:50199200-50209400	Enhancers	Placenta	Placenta
24	chr3:50199400-50202800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:50199400-50204800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr3:50199400-50206400	Enhancers	NHLF	lung
27	chr3:50199800-50202800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:50199800-50202800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:50199800-50202800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:50199800-50203000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:50199800-50204800	Enhancers	Liver	Liver
32	chr3:50200000-50202800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:50200000-50206600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:50200000-50209600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:50200000-50210400	Enhancers	Fetal Brain Male	brain
36	chr3:50200200-50202400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:50200200-50205800	Enhancers	Fetal Kidney	kidney
38	chr3:50200400-50202600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:50200400-50204800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:50200600-50202400	Bivalent Enhancer	Fetal Intestine Small	intestine
41	chr3:50200600-50203800	Enhancers	Spleen	Spleen
42	chr3:50200600-50206000	Enhancers	Fetal Intestine Large	intestine
43	chr3:50200600-50211800	Enhancers	Right Ventricle	heart
44	chr3:50200800-50203400	Flanking Active TSS	Hela-S3	cervix
45	chr3:50200800-50204800	Enhancers	Brain Angular Gyrus	brain
46	chr3:50200800-50204800	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr3:50200800-50205600	Enhancers	Fetal Muscle Trunk	muscle
48	chr3:50200800-50205600	Enhancers	HSMMtube	muscle
49	chr3:50201000-50202400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:50201000-50202400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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