Variant report

Variant	rs2233437
Chromosome Location	chr6:44228162-44228163
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	POU2F2	chr6:44228119-44228644	GM12891	blood:	n/a	n/a
2	POLR2A	chr6:44227445-44228814	GM15510	blood:	n/a	n/a
3	POLR2A	chr6:44227403-44228882	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:44213452-44233528	GM12892	blood:	n/a	n/a
5	EP300	chr6:44228081-44228817	GM12878	blood:	n/a	n/a
6	TBP	chr6:44228125-44228888	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:44213372-44233644	GM12891	blood:	n/a	n/a
8	STAT5A	chr6:44227684-44228812	GM12878	blood:	n/a	chr6:44228157-44228169
9	POLR2A	chr6:44213416-44233519	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:44228047-44228316	K562	blood:	n/a	n/a
11	RELA	chr6:44228130-44228824	GM18951	blood:	n/a	n/a
12	ATF2	chr6:44228004-44228759	GM12878	blood:	n/a	n/a
13	TAF1	chr6:44228153-44228456	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:44213785-44233471	GM12878	blood:	n/a	n/a
15	SP1	chr6:44228110-44228744	GM12878	blood:	n/a	n/a
16	EBF1	chr6:44227749-44228729	GM12878	blood:	n/a	chr6:44228360-44228369 chr6:44228360-44228370 chr6:44228358-44228369 chr6:44228358-44228371
17	POLR2A	chr6:44213479-44233557	GM12892	blood:	n/a	n/a
18	PML	chr6:44227317-44229066	GM12878	blood:	n/a	n/a
19	SPI1	chr6:44227909-44228252	GM12891	blood:	n/a	chr6:44228081-44228094
20	PAX5	chr6:44228006-44228863	GM12878	blood:	n/a	chr6:44228492-44228511
21	EBF1	chr6:44227829-44228760	GM12878	blood:	n/a	chr6:44228360-44228369 chr6:44228360-44228370 chr6:44228358-44228369 chr6:44228358-44228371
22	CHD1	chr6:44227591-44229361	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:44227591-44228786	GM18951	blood:	n/a	n/a
24	BHLHE40	chr6:44228131-44228858	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:44227413-44228427	GM12878	blood:	n/a	n/a
26	BCLAF1	chr6:44227812-44229023	GM12878	blood:	n/a	chr6:44228087-44228096
27	USF2	chr6:44227391-44228460	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:44221854-44228812	GM19193	blood:	n/a	n/a
29	EP300	chr6:44228028-44228765	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:44227960-44228837	GM12892	blood:	n/a	n/a
31	MAX	chr6:44227614-44228746	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:44213632-44233614	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:44227345-44229026	GM12891	blood:	n/a	n/a
34	POLR2A	chr6:44227683-44228362	GM12878	blood:	n/a	n/a
35	MTA3	chr6:44227656-44229165	GM12878	blood:	n/a	n/a
36	CHD2	chr6:44224544-44229859	GM12878	blood:	n/a	chr6:44225411-44225421 chr6:44224708-44224718
37	CTCF	chr6:44227998-44228175	GM12878	blood:	n/a	n/a
38	POU2F2	chr6:44228042-44228643	GM12891	blood:	n/a	n/a
39	RUNX3	chr6:44228078-44228817	GM12878	blood:	n/a	n/a
40	RUNX3	chr6:44228036-44229173	GM12878	blood:	n/a	n/a
41	BCLAF1	chr6:44228058-44228896	GM12878	blood:	n/a	chr6:44228087-44228096
42	POLR2A	chr6:44216490-44233394	GM12878	blood:	n/a	n/a
43	RELA	chr6:44228084-44228850	GM19193	blood:	n/a	n/a
44	NFIC	chr6:44228042-44229007	GM12878	blood:	n/a	n/a
45	MAZ	chr6:44227813-44228952	GM12878	blood:	n/a	n/a
46	STAT5A	chr6:44227458-44229222	GM12878	blood:	n/a	chr6:44228157-44228169
47	ESRRA	chr6:44222591-44234485	GM12878	blood:	n/a	chr6:44225492-44225508 chr6:44225493-44225512 chr6:44225493-44225507 chr6:44225491-44225509 chr6:44231630-44231646 chr6:44225492-44225502
48	NFATC1	chr6:44227818-44228893	GM12878	blood:	n/a	n/a
49	CUX1	chr6:44227838-44229022	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:44220484-44228795	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44225090..44228269-chr6:44308012..44310883,3	K562	blood:
2	chr6:43595119..43596813-chr6:44228044..44230570,2	K562	blood:

Variant related genes	Relation type
NFKBIE	TF binding region
SLC35B2	TF binding region
ENSG00000172432	Chromatin interaction
ENSG00000249481	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs324137	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs325001	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs3799962	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs483536	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs498512	0.81[JPT][hapmap]
rs513688	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs639728	0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs651297	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs730775	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription 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	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers 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	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' 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	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885855	chr6:44223010-44231479	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
12	nsv885856	chr6:44223010-44232920	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
13	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2233437	NT5DC2	trans	cerebellum	SCAN
rs2233437	TCTE1	cis	cerebellum	SCAN
rs2233437	HSP90AB1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44225600-44230800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:44225600-44232600	Weak transcription	Aorta	Aorta
3	chr6:44225800-44229800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:44225800-44230000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:44225800-44230000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:44225800-44230000	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr6:44225800-44230200	Weak transcription	Small Intestine	intestine
8	chr6:44225800-44230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:44225800-44230400	Weak transcription	Right Atrium	heart
10	chr6:44225800-44230400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
11	chr6:44225800-44230400	Weak transcription	HMEC	breast
12	chr6:44225800-44230600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:44225800-44230600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:44225800-44230600	Weak transcription	Ovary	ovary
15	chr6:44225800-44230600	Weak transcription	NHDF-Ad	bronchial
16	chr6:44225800-44230800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:44225800-44230800	Weak transcription	Fetal Kidney	kidney
18	chr6:44225800-44230800	Weak transcription	Psoas Muscle	Psoas
19	chr6:44225800-44230800	Weak transcription	HSMM	muscle
20	chr6:44225800-44231000	Genic enhancers	Spleen	Spleen
21	chr6:44225800-44231400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:44226000-44228400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:44226000-44228600	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr6:44226000-44228600	Strong transcription	Lung	lung
25	chr6:44226000-44229000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:44226000-44229200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:44226000-44229400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:44226000-44229400	Strong transcription	Primary hematopoietic stem cells	blood
29	chr6:44226000-44229400	Strong transcription	Gastric	stomach
30	chr6:44226000-44229600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:44226000-44229800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:44226000-44229800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr6:44226000-44229800	Genic enhancers	Primary B cells from cord blood	blood
34	chr6:44226000-44229800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:44226000-44229800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:44226000-44229800	Strong transcription	Fetal Intestine Large	intestine
37	chr6:44226000-44229800	Strong transcription	Fetal Intestine Small	intestine
38	chr6:44226000-44229800	Weak transcription	A549	lung
39	chr6:44226000-44230000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr6:44226000-44230000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:44226000-44230000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:44226000-44230000	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:44226000-44230000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:44226000-44230200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:44226000-44230200	Weak transcription	Brain Anterior Caudate	brain
46	chr6:44226000-44230200	Weak transcription	NH-A	brain
47	chr6:44226000-44230600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:44226000-44230800	Weak transcription	NHLF	lung
49	chr6:44226000-44231200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:44226200-44228200	Strong transcription	Brain Cingulate Gyrus	brain

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