Variant report

Variant	rs2854510
Chromosome Location	chr19:44074212-44074213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44074168..44077284-chr19:44077377..44081867,9	K562	blood:
2	chr19:44059581..44061634-chr19:44072814..44074549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234465	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000269583	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11407	0.82[ASW][hapmap];0.80[CEU][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2021092	0.90[EUR][1000 genomes]
rs2307187	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs25484	0.82[ASW][hapmap];0.93[CEU][hapmap];0.85[GIH][hapmap];0.88[EUR][1000 genomes]
rs2599442	0.82[CEU][hapmap]
rs2599459	0.85[EUR][1000 genomes]
rs2599464	0.88[EUR][1000 genomes]
rs2682552	1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]
rs2682560	0.82[ASW][hapmap];0.93[CEU][hapmap];0.85[GIH][hapmap];0.88[EUR][1000 genomes]
rs2682562	0.88[EUR][1000 genomes]
rs2682587	0.82[ASW][hapmap];0.80[CEU][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2682588	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2854495	0.85[EUR][1000 genomes]
rs2854496	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]
rs2854497	1.00[CHB][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2854498	0.85[EUR][1000 genomes]
rs2854502	0.88[EUR][1000 genomes]
rs2854505	0.90[EUR][1000 genomes]
rs304729	0.80[CEU][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes]
rs304730	0.81[EUR][1000 genomes]
rs3213251	1.00[ASN][1000 genomes]
rs3213283	0.91[EUR][1000 genomes]
rs3213285	0.90[EUR][1000 genomes]
rs3213289	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213293	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3213321	1.00[CHB][hapmap]
rs3213322	1.00[CHB][hapmap]
rs3213332	0.86[EUR][1000 genomes]
rs3213370	0.86[EUR][1000 genomes]
rs346049	1.00[CHB][hapmap]
rs73556510	1.00[ASN][1000 genomes]
rs73556512	1.00[ASN][1000 genomes]
rs73556542	1.00[ASN][1000 genomes]
rs8104645	1.00[CHB][hapmap]
rs939460	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2854510	STRN4	cis	cerebellum	SCAN
rs2854510	PHLDB3	cis	lesional skin	skin_eQTL
rs2854510	PIH1D1	cis	cerebellum	SCAN
rs2854510	ZNF575	cis	Adipose Subcutaneous	GTEx
rs2854510	BCAT2	cis	cerebellum	SCAN
rs2854510	XRCC1	cis	multi-tissue	Pritchard
rs2854510	LOC653583	cis	multi-tissue	Pritchard
rs2854510	SNRPD2	cis	parietal	SCAN
rs2854510	XRCC1	cis	lymphoblastoid	seeQTL
rs2854510	NANOS2	cis	parietal	SCAN
rs2854510	SLC8A2	cis	cerebellum	SCAN
rs2854510	PHLDB3	cis	normal skin	skin_eQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44039200-44078600	Weak transcription	Hela-S3	cervix
2	chr19:44048400-44078800	Weak transcription	Small Intestine	intestine
3	chr19:44057800-44078800	Weak transcription	HSMMtube	muscle
4	chr19:44058600-44078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:44059000-44076000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:44059200-44078800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:44059800-44078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:44062600-44076000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:44063400-44076200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:44065200-44078600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:44065400-44078600	Weak transcription	Ovary	ovary
12	chr19:44065400-44078800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:44065400-44078800	Weak transcription	Aorta	Aorta
14	chr19:44065800-44078600	Weak transcription	HSMM	muscle
15	chr19:44066000-44078600	Weak transcription	K562	blood
16	chr19:44066200-44078800	Weak transcription	Pancreas	Pancrea
17	chr19:44066600-44076200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:44066600-44078800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:44067000-44078600	Weak transcription	Gastric	stomach
20	chr19:44067200-44075600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:44067200-44076000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:44067200-44076200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:44067200-44078600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:44067200-44078600	Weak transcription	Fetal Kidney	kidney
25	chr19:44067400-44074800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr19:44067400-44075000	Weak transcription	Placenta	Placenta
27	chr19:44067400-44076000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:44067400-44076000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr19:44067400-44076200	Weak transcription	Brain Anterior Caudate	brain
30	chr19:44067400-44078600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:44067400-44078600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:44067400-44078600	Weak transcription	Liver	Liver
33	chr19:44067400-44078600	Weak transcription	Brain Substantia Nigra	brain
34	chr19:44067400-44078600	Weak transcription	Left Ventricle	heart
35	chr19:44067400-44078600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr19:44067400-44078600	Weak transcription	HUVEC	blood vessel
37	chr19:44067400-44078800	Weak transcription	Fetal Heart	heart
38	chr19:44067400-44078800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:44067400-44078800	Weak transcription	Right Ventricle	heart
40	chr19:44067600-44078800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:44067800-44074800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:44067800-44075600	Weak transcription	NHLF	lung
43	chr19:44067800-44077600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:44067800-44078600	Weak transcription	Esophagus	oesophagus
45	chr19:44068000-44075200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:44068000-44077400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:44068000-44078600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr19:44068000-44078600	Weak transcription	Brain Angular Gyrus	brain
49	chr19:44068000-44078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:44068000-44078600	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links