Variant report

Variant	rs11673628
Chromosome Location	chr19:56623066-56623067
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56621941..56623782-chr19:56652294..56654418,2	MCF-7	breast:
2	chr19:56600362..56602994-chr19:56622256..56625120,2	K562	blood:
3	chr19:56599644..56602994-chr19:56620278..56624249,5	K562	blood:
4	chr19:56622447..56624561-chr19:56624820..56626389,2	MCF-7	breast:
5	chr19:56606614..56610711-chr19:56622862..56625649,3	MCF-7	breast:
6	chr19:56617972..56620643-chr19:56620884..56623590,3	MCF-7	breast:
7	chr19:56622659..56624713-chr19:56687287..56689653,2	K562	blood:
8	chr19:56622071..56628058-chr19:56628441..56634693,11	MCF-7	breast:
9	chr19:56622267..56625662-chr19:56649555..56652513,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000142409	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000197487	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1007851	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12981138	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12983086	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450439	0.80[ASN][1000 genomes]
rs2631627	0.81[ASN][1000 genomes]
rs2631628	0.81[ASN][1000 genomes]
rs2631631	0.82[ASN][1000 genomes]
rs2631637	0.85[ASN][1000 genomes]
rs2631640	0.86[ASN][1000 genomes]
rs2637092	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2637094	0.81[ASN][1000 genomes]
rs2637097	0.83[ASN][1000 genomes]
rs2932757	0.83[ASN][1000 genomes]
rs35766803	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs473953	0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs478402	0.85[ASN][1000 genomes]
rs4801294	0.82[ASN][1000 genomes]
rs4801676	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs490345	0.81[ASN][1000 genomes]
rs499083	0.89[CEU][hapmap]
rs504350	0.90[JPT][hapmap]
rs506547	0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs506986	0.89[CEU][hapmap]
rs509897	0.81[ASN][1000 genomes]
rs524778	0.88[ASN][1000 genomes]
rs524829	0.88[ASN][1000 genomes]
rs524988	0.81[ASN][1000 genomes]
rs525827	0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs527715	0.84[ASN][1000 genomes]
rs540900	0.86[JPT][hapmap]
rs546082	0.89[CEU][hapmap]
rs562907	0.88[CEU][hapmap]
rs572851	0.81[ASN][1000 genomes]
rs578990	0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs578991	0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs583330	0.84[ASN][1000 genomes]
rs588574	0.82[JPT][hapmap]
rs592827	0.85[ASN][1000 genomes]
rs609736	0.86[JPT][hapmap]
rs619934	0.86[JPT][hapmap]
rs626821	0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs629544	0.82[ASN][1000 genomes]
rs640654	0.84[ASN][1000 genomes]
rs643133	0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs643174	0.81[ASN][1000 genomes]
rs6509982	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6509983	0.83[AFR][1000 genomes]
rs659424	0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs662308	0.81[ASN][1000 genomes]
rs665082	0.81[ASN][1000 genomes]
rs665857	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs667438	0.84[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs667974	0.87[ASN][1000 genomes]
rs669866	0.85[JPT][hapmap]
rs672824	0.89[CEU][hapmap]
rs677127	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs678540	0.81[ASN][1000 genomes]
rs684653	0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs685117	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7250351	0.84[ASN][1000 genomes]
rs8103672	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9676765	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
16	esv1809307	chr19:56604027-56633623	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv1811581	chr19:56609313-56631618	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
18	esv1824038	chr19:56610449-56636632	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11673628	LOC126208	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:56616000-56626600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr19:56616000-56627000	Enhancers	Liver	Liver
4	chr19:56616000-56627200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr19:56617200-56624400	Weak transcription	Hela-S3	cervix
6	chr19:56617200-56629200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:56617400-56623400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:56618200-56624400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:56618600-56630000	Weak transcription	Dnd41	blood
10	chr19:56618800-56626400	Enhancers	Fetal Thymus	thymus
11	chr19:56619200-56624200	Enhancers	Placenta	Placenta
12	chr19:56619200-56627200	Enhancers	Left Ventricle	heart
13	chr19:56619400-56623200	Enhancers	Ovary	ovary
14	chr19:56619600-56625000	Enhancers	Fetal Heart	heart
15	chr19:56619600-56627200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:56619800-56623800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:56619800-56624800	Enhancers	Fetal Intestine Large	intestine
18	chr19:56619800-56625400	Enhancers	Fetal Lung	lung
19	chr19:56620000-56627000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr19:56620200-56623400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:56620200-56625000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr19:56620400-56625400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr19:56620400-56631000	Enhancers	Pancreas	Pancrea
24	chr19:56620600-56623400	Enhancers	Right Ventricle	heart
25	chr19:56620600-56623800	Weak transcription	Fetal Brain Female	brain
26	chr19:56620600-56625000	Enhancers	Stomach Mucosa	stomach
27	chr19:56620800-56625800	Enhancers	Brain Hippocampus Middle	brain
28	chr19:56620800-56626200	Enhancers	Fetal Muscle Leg	muscle
29	chr19:56620800-56627200	Enhancers	Right Atrium	heart
30	chr19:56620800-56630400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr19:56620800-56631000	Weak transcription	Aorta	Aorta
32	chr19:56621000-56623200	Weak transcription	Primary T cells from cord blood	blood
33	chr19:56621000-56626000	Weak transcription	NHEK	skin
34	chr19:56621000-56630000	Weak transcription	NHDF-Ad	bronchial
35	chr19:56621400-56625400	Enhancers	HUVEC	blood vessel
36	chr19:56621600-56623400	Enhancers	Brain Cingulate Gyrus	brain
37	chr19:56621600-56623600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr19:56621600-56623600	Enhancers	HSMMtube	muscle
39	chr19:56621600-56625000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr19:56621600-56625000	Enhancers	HSMM	muscle
41	chr19:56621600-56625200	Enhancers	Brain Substantia Nigra	brain
42	chr19:56621600-56626600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:56621600-56626600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:56621600-56626800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr19:56621800-56623200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr19:56621800-56623600	Flanking Active TSS	HepG2	liver
47	chr19:56621800-56624000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr19:56621800-56624800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:56621800-56624800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr19:56621800-56625000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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