Variant report

Variant	rs7259967
Chromosome Location	chr19:42378463-42378464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:42375827-42378940	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr19:42374323-42378847	A549	lung:	n/a	n/a
3	POLR2A	chr19:42378437-42378856	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr19:42378397-42378837	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr19:42371518-42378813	U87	brain:	n/a	n/a
6	POLR2A	chr19:42378452-42378821	U87	brain:	n/a	n/a
7	POLR2A	chr19:42375801-42378727	IMR90	lung:	n/a	n/a
8	POLR2A	chr19:42378440-42378798	U87	brain:	n/a	n/a
9	POLR2A	chr19:42377883-42378485	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr19:42363421-42379264	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:42377884-42378905	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr19:42370052-42378775	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr19:42370111-42380312	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr19:42375195-42378820	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr19:42375632-42378850	A549	lung:	n/a	chr19:42377229-42377247 chr19:42376303-42376312 chr19:42377224-42377245 chr19:42377386-42377399
16	POLR2A	chr19:42370118-42378825	A549	lung:	n/a	n/a
17	POLR2A	chr19:42378436-42378521	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:42375672-42379985	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr19:42375534-42378838	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr19:42375296-42379225	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:42375279-42378863	HUVEC	blood vessel:	n/a	n/a
22	BCL3	chr19:42378248-42378904	A549	lung:	n/a	n/a
23	POLR2A	chr19:42374254-42378819	U87	brain:	n/a	n/a
24	POLR2A	chr19:42378372-42378564	HepG2	liver:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42367000..42368909-chr19:42375795..42378988,3	MCF-7	breast:
2	chr19:42375660..42379259-chr19:42380493..42384437,4	MCF-7	breast:
3	chr19:42373799..42381047-chr19:42460989..42465067,14	K562	blood:
4	chr19:42377177..42378851-chr19:42479605..42481434,2	K562	blood:
5	chr19:42375717..42378779-chr19:42460823..42464081,5	MCF-7	breast:
6	chr19:42374516..42378766-chr19:42444244..42446935,5	K562	blood:
7	chr19:42375846..42378575-chr19:42437686..42441355,5	MCF-7	breast:
8	chr19:42373353..42379670-chr19:42459996..42464717,12	K562	blood:
9	chr19:42375885..42381575-chr19:42432655..42439530,9	K562	blood:
10	chr19:42378071..42380066-chr19:42429626..42432415,2	MCF-7	breast:
11	chr19:42377383..42379799-chr19:42454565..42456876,2	MCF-7	breast:
12	chr19:42377500..42380123-chr19:42404788..42407614,2	MCF-7	breast:
13	chr19:42373231..42374863-chr19:42378109..42381070,2	MCF-7	breast:

No data

Variant related genes	Relation type
CD79A	TF binding region
ENSG00000105369	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000076928	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10404939	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10405900	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10408367	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10414823	0.96[CHB][hapmap]
rs10415452	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10416824	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10417985	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10500284	1.00[CHB][hapmap]
rs12461099	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12461131	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12976571	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12979253	0.95[CHB][hapmap]
rs12984383	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1366610	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1428922	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1457144	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1870092	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2008798	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2075749	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075750	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2075752	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2075754	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2199829	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs2290695	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2305809	1.00[CHB][hapmap]
rs3786536	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3786538	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3810153	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3922888	1.00[CHB][hapmap]
rs4803511	1.00[CHB][hapmap]
rs4803512	0.95[CHB][hapmap]
rs58857981	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6509002	0.91[CHB][hapmap]
rs7250787	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251336	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs7251960	0.82[CHB][hapmap]
rs7254214	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7257666	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7258163	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7259596	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs734107	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs73549152	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8102670	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8104958	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs8106505	0.96[CHB][hapmap]
rs8113283	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs8113641	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs873282	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs882520	0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs891167	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs899662	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs930102	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription 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
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv932623	chr19:42370540-42378620	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7259967	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42367600-42379200	Weak transcription	Fetal Brain Male	brain
2	chr19:42369600-42386400	Weak transcription	Fetal Kidney	kidney
3	chr19:42373800-42381400	Enhancers	Primary hematopoietic stem cells	blood
4	chr19:42374600-42379800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr19:42374600-42386600	Weak transcription	Right Atrium	heart
6	chr19:42374800-42379600	Weak transcription	K562	blood
7	chr19:42374800-42380600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:42374800-42381400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:42374800-42381400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr19:42374800-42381400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:42374800-42381400	Weak transcription	Small Intestine	intestine
12	chr19:42374800-42381800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:42375000-42381200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:42375400-42380200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr19:42375400-42386200	Weak transcription	Hela-S3	cervix
16	chr19:42376000-42381000	Weak transcription	HepG2	liver
17	chr19:42376000-42386400	Weak transcription	Brain Anterior Caudate	brain
18	chr19:42376000-42386400	Weak transcription	Fetal Lung	lung
19	chr19:42376000-42386600	Weak transcription	HSMMtube	muscle
20	chr19:42376200-42378800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:42376200-42379000	Weak transcription	Aorta	Aorta
22	chr19:42376200-42379400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:42376200-42379400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:42376200-42379400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:42376200-42380200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:42376200-42380600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:42376200-42381000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr19:42376200-42381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:42376200-42386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:42376200-42386400	Weak transcription	Psoas Muscle	Psoas
31	chr19:42376400-42379400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:42376400-42379600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr19:42376400-42379800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:42376400-42379800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:42376400-42380600	Weak transcription	NHEK	skin
36	chr19:42376400-42380800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr19:42376400-42380800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:42376400-42381000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr19:42376400-42381800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr19:42376400-42386400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:42376400-42386400	Weak transcription	Brain Substantia Nigra	brain
42	chr19:42376400-42386400	Weak transcription	Colon Smooth Muscle	Colon
43	chr19:42376400-42386400	Weak transcription	Esophagus	oesophagus
44	chr19:42376400-42386400	Weak transcription	Gastric	stomach
45	chr19:42376400-42386400	Weak transcription	Left Ventricle	heart
46	chr19:42376400-42386400	Weak transcription	HMEC	breast
47	chr19:42376400-42386400	Weak transcription	HUVEC	blood vessel
48	chr19:42376600-42379600	Enhancers	Primary B cells from cord blood	blood
49	chr19:42376600-42379600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr19:42376600-42379600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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