Variant report

Variant	rs3780221
Chromosome Location	chr9:19059395-19059396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:19057659..19060410-chr9:19065163..19067075,2	MCF-7	breast:
2	chr9:19047815..19051920-chr9:19059241..19062627,4	MCF-7	breast:
3	chr9:19050026..19052622-chr9:19058219..19060617,2	K562	blood:
4	chr9:19048116..19054448-chr9:19056568..19061765,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155876	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10123520	0.84[CHB][hapmap]
rs10465047	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10511670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10511671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs10811113	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10963906	0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs10963919	0.80[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10963920	0.85[ASN][1000 genomes]
rs10963923	1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs10963929	0.90[ASN][1000 genomes]
rs10963930	0.93[ASN][1000 genomes]
rs10963943	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963944	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963950	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10963953	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10963955	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10963958	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10963962	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10963964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs10963966	0.82[ASN][1000 genomes]
rs11788135	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12238548	0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs13284130	0.88[ASN][1000 genomes]
rs13291632	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13298563	0.83[CHB][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs13302453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16937267	0.82[CHB][hapmap]
rs16937320	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1932451	0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs2291502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34490350	0.82[ASN][1000 genomes]
rs34507853	0.80[ASN][1000 genomes]
rs35448309	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35553284	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35874966	0.82[ASN][1000 genomes]
rs36087651	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7026759	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7031392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[ASN][1000 genomes]
rs7040525	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71508774	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71508775	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71508776	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73645573	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7467137	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs7852850	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7864553	0.87[ASN][1000 genomes]
rs7865126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19050600-19060800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:19050800-19074200	Weak transcription	Lung	lung
6	chr9:19051400-19066400	Weak transcription	Colonic Mucosa	Colon
7	chr9:19051600-19074400	Weak transcription	Spleen	Spleen
8	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:19051800-19059400	Weak transcription	HSMMtube	muscle
10	chr9:19051800-19070200	Weak transcription	Fetal Kidney	kidney
11	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:19052000-19061800	Weak transcription	Stomach Mucosa	stomach
13	chr9:19052000-19062600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:19052000-19075200	Weak transcription	Right Ventricle	heart
15	chr9:19052400-19077000	Weak transcription	Pancreas	Pancrea
16	chr9:19052600-19065000	Weak transcription	Small Intestine	intestine
17	chr9:19052800-19061600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:19052800-19062600	Weak transcription	Brain Angular Gyrus	brain
19	chr9:19052800-19074400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:19052800-19075600	Weak transcription	Aorta	Aorta
21	chr9:19052800-19092400	Weak transcription	Fetal Brain Male	brain
22	chr9:19053400-19059400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr9:19053600-19065000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:19055000-19072600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:19055200-19065600	Strong transcription	Placenta	Placenta
29	chr9:19055400-19065600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr9:19055400-19065600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:19055600-19082600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:19055600-19091200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr9:19055800-19065400	Strong transcription	Dnd41	blood
34	chr9:19055800-19065400	Strong transcription	HUVEC	blood vessel
35	chr9:19055800-19079800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:19055800-19085200	Strong transcription	Liver	Liver
37	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:19056000-19086000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr9:19056000-19091200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr9:19056000-19096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:19056200-19060800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr9:19056200-19063000	Strong transcription	Osteobl	bone
45	chr9:19056200-19065600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:19056400-19065400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:19056400-19073600	Strong transcription	Hela-S3	cervix
48	chr9:19056600-19060200	Strong transcription	Brain Hippocampus Middle	brain
49	chr9:19056600-19060400	Strong transcription	Fetal Muscle Leg	muscle
50	chr9:19056600-19060400	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links