Variant report

Variant	rs2227278
Chromosome Location	chr19:36206050-36206051
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:141)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:141 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr19:36203117-36208944	GM12878	blood:	n/a	n/a
2	CEBPB	chr19:36205905-36206144	IMR90	lung:	n/a	n/a
3	POLR2A	chr19:36203385-36212934	GM12892	blood:	n/a	n/a
4	CTCF	chr19:36205940-36206090	GM12874	blood:	n/a	n/a
5	POLR2A	chr19:36205896-36206548	GM12891	blood:	n/a	n/a
6	CTCF	chr19:36205960-36206110	GM12874	blood:	n/a	n/a
7	CTCF	chr19:36205960-36206110	GM12801	blood:	n/a	n/a
8	SIN3A	chr19:36205820-36206204	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:36202991-36212995	GM12878	blood:	n/a	n/a
10	CTCF	chr19:36205980-36206130	HL-60	blood:	n/a	n/a
11	SMC3	chr19:36205852-36206245	GM12878	blood:	n/a	n/a
12	CTCF	chr19:36205960-36206110	HAc	cerebellar:	n/a	n/a
13	MXI1	chr19:36205641-36206224	GM12878	blood:	n/a	n/a
14	CTCF	chr19:36205960-36206110	HPAF	blood vessel:	n/a	n/a
15	CTCF	chr19:36205876-36206182	K562	blood:	n/a	n/a
16	CTCF	chr19:36205940-36206090	Caco-2	colon:	n/a	n/a
17	CEBPB	chr19:36205851-36206199	HepG2	liver:	n/a	n/a
18	CTCF	chr19:36205940-36206090	GM12867	blood:	n/a	n/a
19	ZNF143	chr19:36205975-36206156	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAZ	chr19:36205718-36206176	GM12878	blood:	n/a	n/a
21	CTCF	chr19:36205960-36206110	WERI-Rb-1	eye:	n/a	n/a
22	CTCF	chr19:36205988-36206104	GM20000	blood:	n/a	n/a
23	CTCF	chr19:36206020-36206170	HCT-116	colon:	n/a	n/a
24	CTCF	chr19:36205960-36206110	GM12871	blood:	n/a	n/a
25	CTCF	chr19:36205925-36206180	GM19240	blood:	n/a	n/a
26	CTCF	chr19:36205980-36206130	WERI-Rb-1	eye:	n/a	n/a
27	CTCF	chr19:36205980-36206130	Caco-2	colon:	n/a	n/a
28	CEBPB	chr19:36205932-36206123	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:36202895-36208735	GM12878	blood:	n/a	n/a
30	CTCF	chr19:36205920-36206070	HRPEpiC	eye:	n/a	n/a
31	CTCF	chr19:36205930-36206169	GM12891	blood:	n/a	n/a
32	CTCF	chr19:36205973-36206162	GM13976	blood:	n/a	n/a
33	CTCF	chr19:36205932-36206187	GM12892	blood:	n/a	n/a
34	MAX	chr19:36205982-36206215	H1-hESC	embryonic stem cell:	n/a	n/a
35	CHD1	chr19:36205256-36206141	GM12878	blood:	n/a	n/a
36	CTCF	chr19:36205979-36206110	GM13977	blood:	n/a	n/a
37	CTCF	chr19:36205980-36206130	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr19:36205960-36206110	GM12875	blood:	n/a	n/a
39	CTCF	chr19:36205940-36206090	GM12873	blood:	n/a	n/a
40	CTCF	chr19:36205940-36206090	HEK293	kidney:	n/a	n/a
41	USF1	chr19:36206025-36206249	HepG2	liver:	n/a	n/a
42	CTCF	chr19:36205920-36206070	AG04450	lung:	n/a	n/a
43	CTCF	chr19:36205980-36206130	GM12873	blood:	n/a	n/a
44	CTCF	chr19:36205877-36206141	K562	blood:	n/a	n/a
45	CTCF	chr19:36205837-36206192	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr19:36205960-36206110	GM12873	blood:	n/a	n/a
47	CTCF	chr19:36205900-36206050	HUVEC	blood vessel:	n/a	n/a
48	CTCF	chr19:36205964-36206104	HepG2	liver:	n/a	n/a
49	POLR2A	chr19:36203580-36208801	GM12891	blood:	n/a	n/a
50	RUNX3	chr19:36204888-36206220	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:36201857..36203426-chr19:36205188..36208060,2	MCF-7	breast:
2	chr19:35752101..35756218-chr19:36205472..36209304,3	MCF-7	breast:
3	chr19:36205479..36207948-chr19:36393989..36396293,2	K562	blood:
4	chr19:36205889..36208076-chr19:36208426..36210267,2	MCF-7	breast:
5	chr19:36034638..36039287-chr19:36205354..36210335,7	K562	blood:
6	chr19:36039298..36042202-chr19:36205627..36208173,3	K562	blood:
7	chr19:36040674..36043456-chr19:36205595..36207863,3	MCF-7	breast:
8	chr19:36047138..36050303-chr19:36204932..36209680,5	K562	blood:
9	chr19:36035457..36038261-chr19:36205897..36210098,5	MCF-7	breast:
10	chr19:36204664..36206261-chr19:36206379..36207962,2	K562	blood:
11	chr19:36205476..36213390-chr19:36226310..36233646,27	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272333	TF binding region
KMT2B	TF binding region
ENSG00000105663	Chromatin interaction
ENSG00000236144	Chromatin interaction
ENSG00000126246	Chromatin interaction
ENSG00000268947	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000105677	Chromatin interaction
ENSG00000105675	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11546662	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11546665	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11882996	0.80[ASW][hapmap]
rs16970649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17776834	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2234360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267585	0.86[EUR][1000 genomes]
rs2267586	0.88[CEU][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs2285420	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs231217	0.83[AMR][1000 genomes]
rs2871893	0.84[EUR][1000 genomes]
rs2871894	0.84[EUR][1000 genomes]
rs34562867	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817622	1.00[CHB][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3893069	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4580318	0.86[EUR][1000 genomes]
rs4992668	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56849855	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57180990	0.86[EUR][1000 genomes]
rs58142685	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58255615	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58496446	0.86[EUR][1000 genomes]
rs58952294	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61254015	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61351824	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61375471	0.86[EUR][1000 genomes]
rs73590543	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590544	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73590559	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590561	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590564	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73590568	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590576	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590585	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590591	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590598	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73592416	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73592448	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73592461	0.80[EUR][1000 genomes]
rs73599271	0.85[EUR][1000 genomes]
rs73599272	0.83[EUR][1000 genomes]
rs73599274	0.83[EUR][1000 genomes]
rs73599279	0.84[EUR][1000 genomes]
rs73599281	0.84[EUR][1000 genomes]
rs73599286	0.86[EUR][1000 genomes]
rs73599289	0.86[EUR][1000 genomes]
rs73600880	0.86[EUR][1000 genomes]
rs73600881	0.86[EUR][1000 genomes]
rs73600885	0.87[EUR][1000 genomes]
rs73600892	0.84[EUR][1000 genomes]
rs73600893	0.86[EUR][1000 genomes]
rs73600899	0.93[EUR][1000 genomes]
rs73602803	0.94[EUR][1000 genomes]
rs73602804	0.94[EUR][1000 genomes]
rs73602806	0.94[EUR][1000 genomes]
rs73602823	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs73602827	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73602832	0.99[EUR][1000 genomes]
rs73602833	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2227278	PLD3	cis	cerebellum	SCAN
rs2227278	DPF1	cis	parietal	SCAN
rs2227278	TEX101	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36194000-36206600	Weak transcription	Brain Angular Gyrus	brain
2	chr19:36194000-36206800	Weak transcription	Right Atrium	heart
3	chr19:36194000-36206800	Weak transcription	Osteobl	bone
4	chr19:36194600-36206200	Weak transcription	Right Ventricle	heart
5	chr19:36195400-36206600	Weak transcription	Gastric	stomach
6	chr19:36201200-36206600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:36201200-36207000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr19:36201400-36206400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr19:36201600-36207000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr19:36201600-36207200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:36201800-36206800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr19:36202200-36206400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:36202200-36206400	Weak transcription	Brain Anterior Caudate	brain
14	chr19:36202200-36207000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr19:36202400-36206200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:36202400-36206400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:36202600-36206200	Weak transcription	Esophagus	oesophagus
18	chr19:36202600-36206200	Weak transcription	A549	lung
19	chr19:36202600-36206400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:36202600-36206600	Weak transcription	NHEK	skin
21	chr19:36203200-36207400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr19:36203600-36207600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr19:36204000-36206400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:36204200-36206400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:36204200-36206600	Weak transcription	Small Intestine	intestine
26	chr19:36204600-36206600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:36204600-36208400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:36204800-36206200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:36204800-36206600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:36204800-36206800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr19:36204800-36206800	Enhancers	Pancreas	Pancrea
32	chr19:36204800-36206800	Weak transcription	K562	blood
33	chr19:36205000-36206600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:36205000-36207000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:36205200-36206200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
36	chr19:36205200-36206200	Enhancers	HepG2	liver
37	chr19:36205200-36206600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
38	chr19:36205200-36206600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr19:36205200-36206600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:36205200-36206600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr19:36205200-36206600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:36205200-36207000	Enhancers	Primary T cells from cord blood	blood
43	chr19:36205200-36208200	Flanking Active TSS	GM12878-XiMat	blood
44	chr19:36205400-36206200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:36205400-36206200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr19:36205400-36206400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
47	chr19:36205400-36206600	Enhancers	H9 Cell Line	embryonic stem cell
48	chr19:36205400-36206600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr19:36205400-36206800	Enhancers	Stomach Smooth Muscle	stomach
50	chr19:36205600-36206200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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