Variant report

Variant	rs4744436
Chromosome Location	chr9:97831581-97831582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97830414..97832862-chr9:97837020..97839088,2	K562	blood:
2	chr9:97825460..97828452-chr9:97831131..97835733,4	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1004373	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10117370	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10119512	0.91[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10121760	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10123819	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1020963	0.81[CEU][hapmap]
rs10512253	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10761364	0.82[CEU][hapmap];0.88[AMR][1000 genomes]
rs10761366	0.92[AMR][1000 genomes]
rs10761368	0.81[CEU][hapmap]
rs10993427	0.86[AMR][1000 genomes]
rs10993464	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10993467	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1113102	0.92[AMR][1000 genomes]
rs1412488	0.81[CEU][hapmap]
rs1564234	0.91[CEU][hapmap]
rs1571894	0.91[CEU][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes]
rs1571895	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs2061800	0.83[JPT][hapmap];0.92[AMR][1000 genomes]
rs2404302	0.91[CEU][hapmap];0.94[YRI][hapmap]
rs2404305	0.91[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes]
rs2404456	0.91[CEU][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3802454	0.91[CEU][hapmap]
rs3802456	0.83[CEU][hapmap];0.88[AMR][1000 genomes]
rs3858089	0.82[AMR][1000 genomes]
rs4537362	0.91[CEU][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes]
rs4743979	0.91[CEU][hapmap];0.83[JPT][hapmap];0.97[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743980	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743981	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743982	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743984	0.82[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744422	0.83[CEU][hapmap]
rs4744423	0.83[CEU][hapmap];0.88[AMR][1000 genomes]
rs4744424	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs4744425	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs4744426	0.91[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744428	0.96[AMR][1000 genomes]
rs4744430	0.83[CEU][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744431	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744432	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744433	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744435	0.92[CEU][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6479588	0.83[CEU][hapmap]
rs6479591	0.91[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes]
rs6479592	0.91[CEU][hapmap];0.83[JPT][hapmap];0.97[YRI][hapmap];0.92[AMR][1000 genomes]
rs7020709	0.92[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7021351	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs7022452	0.91[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes]
rs7048786	0.91[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7048941	0.91[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7851173	0.91[CEU][hapmap]
rs7854831	0.82[AMR][1000 genomes]
rs7857679	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7862156	0.82[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7863291	0.91[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7871218	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7873567	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs962229	0.83[JPT][hapmap]

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	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	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4744436	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
3	chr9:97820400-97840800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:97820400-97843000	Weak transcription	Primary T cells from cord blood	blood
5	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr9:97821000-97838400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:97821200-97839000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:97821200-97839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:97821400-97843200	Weak transcription	Fetal Brain Female	brain
10	chr9:97821800-97835600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:97822000-97834600	Strong transcription	Hela-S3	cervix
12	chr9:97822200-97833200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:97822800-97831600	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr9:97822800-97832800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
15	chr9:97822800-97845400	Weak transcription	Primary B cells from cord blood	blood
16	chr9:97823600-97834600	Strong transcription	NH-A	brain
17	chr9:97823600-97845000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:97824200-97832800	Strong transcription	Adipose Nuclei	Adipose
19	chr9:97824600-97832200	Strong transcription	Fetal Lung	lung
20	chr9:97824800-97832000	Enhancers	Fetal Heart	heart
21	chr9:97824800-97844600	Weak transcription	Fetal Thymus	thymus
22	chr9:97825200-97841000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr9:97825800-97839200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:97825800-97843400	Weak transcription	Thymus	Thymus
26	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:97826000-97842800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr9:97826200-97843200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:97826200-97847400	Weak transcription	HUVEC	blood vessel
30	chr9:97826400-97842800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:97826400-97844200	Weak transcription	GM12878-XiMat	blood
32	chr9:97826600-97835200	Weak transcription	Spleen	Spleen
33	chr9:97827000-97839600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:97827600-97832200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:97827600-97832400	Weak transcription	Colonic Mucosa	Colon
36	chr9:97827600-97835600	Enhancers	Right Atrium	heart
37	chr9:97827800-97833400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:97827800-97841400	Genic enhancers	Liver	Liver
39	chr9:97828200-97832800	Weak transcription	Small Intestine	intestine
40	chr9:97828200-97838800	Strong transcription	Fetal Intestine Large	intestine
41	chr9:97828600-97832000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:97828800-97832200	Strong transcription	Fetal Muscle Leg	muscle
43	chr9:97828800-97832600	Genic enhancers	Brain Anterior Caudate	brain
44	chr9:97828800-97833200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:97829200-97831800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:97829200-97831800	Genic enhancers	HSMM	muscle
47	chr9:97829200-97834400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:97829200-97838400	Genic enhancers	Brain Hippocampus Middle	brain
49	chr9:97829400-97832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:97829400-97833400	Genic enhancers	NHDF-Ad	bronchial

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