Variant report

Variant	rs4744411
Chromosome Location	chr9:97689045-97689046
allele	A/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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97687410..97690571-chr9:97710837..97713862,3	MCF-7	breast:
2	chr17:58662561..58665410-chr9:97687576..97689964,2	MCF-7	breast:
3	chr9:97687301..97689149-chr9:97775376..97777317,2	MCF-7	breast:
4	chr9:97687308..97690068-chr9:97855270..97858001,3	MCF-7	breast:
5	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
6	chr9:97566500..97569295-chr9:97687773..97689488,3	MCF-7	breast:
7	chr9:97688111..97690470-chr9:97723342..97725072,2	MCF-7	breast:
8	chr9:97685017..97689714-chr9:97737820..97743340,6	MCF-7	breast:
9	chr9:97440898..97443668-chr9:97686609..97689428,2	MCF-7	breast:
10	chr9:97688794..97691032-chr9:97848721..97850468,2	MCF-7	breast:
11	chr9:97572097..97590438-chr9:97672990..97690806,63	MCF-7	breast:
12	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
13	chr9:97687078..97690879-chr9:97725543..97729239,3	MCF-7	breast:
14	chr9:97688725..97690345-chr9:97748989..97750908,2	MCF-7	breast:
15	chr9:97688635..97691116-chr9:97722109..97725030,2	MCF-7	breast:
16	chr9:97688920..97691846-chr9:97741162..97743776,2	K562	blood:
17	chr9:97393231..97394953-chr9:97687496..97690303,2	MCF-7	breast:
18	chr9:97559408..97562110-chr9:97687505..97689946,2	MCF-7	breast:
19	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:
20	chr9:97627475..97632236-chr9:97687625..97689828,4	MCF-7	breast:
21	chr9:97687964..97690417-chr9:97736353..97738694,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230815	Chromatin interaction
ENSG00000252153	Chromatin interaction
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10217143	0.84[CHB][hapmap]
rs1045276	0.81[YRI][hapmap]
rs10491560	0.81[YRI][hapmap]
rs10761361	0.84[CHB][hapmap]
rs10821410	0.81[CHB][hapmap]
rs10821413	0.81[CHB][hapmap]
rs10821415	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10993365	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10993370	0.80[CEU][hapmap]
rs10993372	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10993377	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10993387	0.81[CHB][hapmap]
rs10993394	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993397	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10993398	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10993418	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1123534	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11787821	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12235316	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs183066	0.92[CEU][hapmap]
rs2183958	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2584806	0.92[CEU][hapmap]
rs35487382	0.81[EUR][1000 genomes]
rs356131	0.96[CEU][hapmap]
rs391784	0.96[CEU][hapmap]
rs4385527	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs446540	0.92[CEU][hapmap]
rs4744378	0.96[CEU][hapmap]
rs4744403	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7033633	0.85[YRI][hapmap]
rs7851726	0.92[CEU][hapmap]
rs7853195	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7862219	0.84[CHB][hapmap]
rs7864171	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7865239	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7866848	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:97680400-97698000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:97680600-97700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:97682000-97713800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:97682200-97691200	Enhancers	Placenta	Placenta
7	chr9:97684200-97699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:97684800-97690000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:97684800-97711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:97685000-97690400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:97685200-97689200	Weak transcription	GM12878-XiMat	blood
12	chr9:97685200-97690600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:97685200-97693000	Weak transcription	Small Intestine	intestine
14	chr9:97685200-97714600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:97685400-97690200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr9:97685400-97690600	Weak transcription	HUVEC	blood vessel
17	chr9:97685600-97690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:97685600-97699600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:97685800-97689800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:97685800-97690000	Weak transcription	Right Ventricle	heart
21	chr9:97685800-97690400	Weak transcription	Fetal Lung	lung
22	chr9:97685800-97693600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:97686000-97690400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:97686000-97690800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:97686000-97691400	Weak transcription	Spleen	Spleen
26	chr9:97686000-97698800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:97686200-97689800	Weak transcription	NH-A	brain
28	chr9:97686200-97690000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:97686200-97690200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:97686200-97690400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:97686200-97690800	Strong transcription	Primary T cells from cord blood	blood
32	chr9:97686200-97694200	Genic enhancers	A549	lung
33	chr9:97686400-97690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:97686400-97690000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr9:97686400-97690200	Weak transcription	Brain Substantia Nigra	brain
36	chr9:97686400-97690400	Weak transcription	Brain Angular Gyrus	brain
37	chr9:97686400-97691600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:97686400-97695200	Weak transcription	Ovary	ovary
39	chr9:97686600-97689600	Weak transcription	Left Ventricle	heart
40	chr9:97686600-97689600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:97686600-97689800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:97686600-97690000	Weak transcription	Brain Anterior Caudate	brain
43	chr9:97686600-97690200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:97686600-97690200	Weak transcription	Brain Hippocampus Middle	brain
45	chr9:97686600-97690600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:97686600-97691200	Weak transcription	Right Atrium	heart
47	chr9:97686800-97689600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr9:97686800-97689800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:97686800-97689800	Weak transcription	NHLF	lung
50	chr9:97686800-97690000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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