Variant report

Variant	rs2844480
Chromosome Location	chr6:31564821-31564822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:31564772-31565114	HepG2	liver:	n/a	n/a
2	MAX	chr6:31564765-31565090	K562	blood:	n/a	chr6:31564923-31564933
3	CTCF	chr6:31564780-31564930	HFF-Myc	foreskin:	n/a	n/a
4	CTCF	chr6:31564577-31565370	A549	lung:	n/a	n/a
5	SMC3	chr6:31564769-31565124	HepG2	liver:	n/a	chr6:31564946-31564960
6	MAX	chr6:31564702-31565182	MCF-7	breast:	n/a	chr6:31564923-31564933
7	CTCF	chr6:31564793-31565110	HUVEC	blood vessel:	n/a	n/a
8	ZNF143	chr6:31564794-31565106	GM12878	blood:	n/a	n/a
9	RAD21	chr6:31564716-31565228	HCT-116	colon:	n/a	n/a
10	CTCF	chr6:31564820-31564970	HCT-116	colon:	n/a	n/a
11	RAD21	chr6:31564688-31565161	HepG2	liver:	n/a	n/a
12	RAD21	chr6:31564762-31565091	SK-N-SH_RA	brain:	n/a	n/a
13	RAD21	chr6:31564700-31565125	GM12878	blood:	n/a	n/a
14	RAD21	chr6:31564759-31565108	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr6:31564820-31564970	NB4	blood:	n/a	n/a
16	ARID3A	chr6:31564819-31565097	HepG2	liver:	n/a	n/a
17	CTCF	chr6:31564820-31564970	BJ	skin:	n/a	n/a
18	CTCF	chr6:31564812-31565014	A549	lung:	n/a	n/a
19	CTCF	chr6:31564662-31565188	MCF-7	breast:	n/a	n/a
20	CTCF	chr6:31564700-31564850	WI-38	lung:	n/a	n/a
21	CTCF	chr6:31564662-31565203	K562	blood:	n/a	n/a
22	CTCF	chr6:31564820-31564970	NHEK	skin:	n/a	n/a
23	CTCF	chr6:31564800-31564950	NHEK	skin:	n/a	n/a
24	SMC3	chr6:31564565-31565208	SK-N-SH	brain:	n/a	chr6:31564946-31564960
25	MYC	chr6:31564771-31565097	MCF10A-Er-Src	breast:	n/a	chr6:31564923-31564933
26	SMC3	chr6:31564770-31565124	Hela-S3	cervix:	n/a	chr6:31564946-31564960
27	RAD21	chr6:31564743-31565092	GM12878	blood:	n/a	n/a
28	FOXM1	chr6:31564691-31565170	GM12878	blood:	n/a	n/a
29	MYC	chr6:31564738-31565085	HUVEC	blood vessel:	n/a	chr6:31564923-31564933
30	MYC	chr6:31564768-31565128	K562	blood:	n/a	chr6:31564923-31564933
31	BCLAF1	chr6:31564769-31565167	GM12878	blood:	n/a	n/a
32	RAD21	chr6:31564782-31565042	GM12878	blood:	n/a	n/a
33	CTCF	chr6:31564820-31564970	HCM	heart:	n/a	n/a
34	MXI1	chr6:31564555-31565224	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr6:31564798-31565168	K562	blood:	n/a	n/a
36	CTCF	chr6:31564800-31564950	HFF	foreskin:	n/a	n/a
37	CTCF	chr6:31564731-31565076	A549	lung:	n/a	n/a
38	CTCF	chr6:31564626-31565226	SK-N-SH	brain:	n/a	n/a
39	CTCF	chr6:31564820-31564970	GM12871	blood:	n/a	n/a
40	ZNF143	chr6:31564820-31565055	K562	blood:	n/a	n/a
41	CTCF	chr6:31564796-31565017	SK-N-SH_RA	brain:	n/a	n/a
42	CTCF	chr6:31564820-31564970	GM12869	blood:	n/a	n/a
43	USF2	chr6:31564747-31565051	GM12878	blood:	n/a	n/a
44	RAD21	chr6:31564745-31565094	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr6:31564820-31564970	GM12865	blood:	n/a	n/a
46	RAD21	chr6:31564712-31565231	HCT-116	colon:	n/a	n/a
47	CTCF	chr6:31564774-31565109	IMR90	lung:	n/a	n/a
48	ATF1	chr6:31564800-31565110	K562	blood:	n/a	n/a
49	CTCF	chr6:31564732-31565043	H1-hESC	embryonic stem cell:	n/a	n/a
50	SMC3	chr6:31564759-31565136	K562	blood:	n/a	chr6:31564946-31564960

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31549450..31550019-chr6:31564413..31565383,2	NB4	blood:
2	chr6:31557562..31560415-chr6:31563588..31566360,2	K562	blood:
3	chr6:31511774..31515264-chr6:31563314..31566638,3	K562	blood:
4	chr6:31514120..31515023-chr6:31564501..31565420,3	MCF-7	breast:
5	chr6:31548213..31551482-chr6:31564598..31567981,3	K562	blood:
6	chr6:31548122..31548776-chr6:31564766..31565341,2	K562	blood:
7	chr6:31544984..31547805-chr6:31562709..31565695,2	MCF-7	breast:
8	chr6:31508128..31511656-chr6:31563517..31568098,6	K562	blood:
9	chr6:31541833..31544710-chr6:31563226..31565455,2	K562	blood:
10	chr6:31514190..31515824-chr6:31564460..31565848,12	K562	blood:
11	chr6:31513067..31517986-chr6:31563374..31568109,9	K562	blood:

No data

Variant related genes	Relation type
NCR3	TF binding region
ENSG00000227507	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000232810	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000265236	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12663590	0.81[AMR][1000 genomes]
rs1799964	0.85[EUR][1000 genomes]
rs28732146	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
4	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
5	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
6	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer 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	376 gene(s)	inside rSNPs	diseases
7	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised 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	378 gene(s)	inside rSNPs	diseases
8	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	378 gene(s)	inside rSNPs	diseases
9	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
10	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
12	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
13	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
14	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
15	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2844480	HIST1H1B	cis	cerebellum	SCAN
rs2844480	HIST1H2AM	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31550000-31583200	Weak transcription	Right Atrium	heart
2	chr6:31557600-31566200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:31560800-31566000	Weak transcription	Spleen	Spleen
4	chr6:31560800-31568200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:31561000-31566800	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:31561000-31566800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:31561000-31568400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:31561200-31565400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:31561200-31565400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr6:31561200-31566000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:31561200-31566000	Weak transcription	Dnd41	blood
12	chr6:31561200-31566800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr6:31561200-31566800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:31561600-31566000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:31561600-31566800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr6:31561800-31566000	Weak transcription	GM12878-XiMat	blood
17	chr6:31563400-31565200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:31563600-31565200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:31563600-31565400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:31563600-31565400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr6:31563600-31566400	Enhancers	Primary T cells from cord blood	blood
22	chr6:31563600-31566800	Enhancers	Fetal Thymus	thymus
23	chr6:31563800-31566600	Enhancers	Primary B cells from cord blood	blood
24	chr6:31563800-31567000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr6:31564400-31565000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:31564400-31565200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:31564400-31566400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:31564400-31566600	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr6:31564600-31565000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:31564600-31565000	Enhancers	Thymus	Thymus
31	chr6:31564600-31565000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr6:31564800-31566200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:31564800-31566800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links