Variant report

Variant	rs4744422
Chromosome Location	chr9:97770527-97770528
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97769222..97771704-chr9:97773500..97776242,3	K562	blood:
2	chr9:97769757..97772435-chr9:97816536..97818768,2	K562	blood:
3	chr11:73679741..73681379-chr9:97769942..97771731,2	MCF-7	breast:
4	chr9:97501974..97503551-chr9:97768873..97771457,2	MCF-7	breast:
5	chr9:97733399..97735846-chr9:97769206..97770842,2	MCF-7	breast:
6	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
7	chr17:57913990..57916266-chr9:97769436..97771085,2	MCF-7	breast:
8	chr9:97563450..97566296-chr9:97770387..97772298,3	MCF-7	breast:
9	chr9:97767984..97771413-chr9:97863181..97865279,3	MCF-7	breast:
10	chr9:97769187..97771943-chr9:97834202..97836015,2	MCF-7	breast:
11	chr9:97543390..97547292-chr9:97769751..97772749,5	MCF-7	breast:
12	chr9:97634532..97637191-chr9:97769954..97772571,2	MCF-7	breast:
13	chr9:97768459..97771257-chr9:97817268..97820157,2	K562	blood:
14	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
15	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:
16	chr9:97769731..97772071-chr9:97808769..97812479,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255847	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000207617	Chromatin interaction
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1004373	0.91[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs10119512	0.90[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs10123819	0.80[AMR][1000 genomes]
rs1020963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10512253	0.83[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs10761364	0.81[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761366	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10761368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10761369	0.81[EUR][1000 genomes]
rs10761372	0.90[ASN][1000 genomes]
rs10821433	0.89[JPT][hapmap]
rs10993427	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10993456	0.90[JPT][hapmap]
rs10993464	0.80[AMR][1000 genomes]
rs10993467	0.80[AMR][1000 genomes]
rs1113102	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12339639	0.90[JPT][hapmap]
rs12346261	0.91[JPT][hapmap]
rs1412488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1564234	0.91[CEU][hapmap];0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1571894	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1571895	0.90[CEU][hapmap];0.88[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061800	0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2404302	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs2404305	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2404456	0.91[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs3802454	0.91[CEU][hapmap];0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3802456	0.83[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4537362	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743979	0.91[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs4743980	0.80[AMR][1000 genomes]
rs4743981	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4743982	0.80[AMR][1000 genomes]
rs4743984	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs4744423	0.83[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744424	0.91[CEU][hapmap];0.84[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744425	0.91[CEU][hapmap];0.83[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744426	0.90[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs4744428	0.80[AMR][1000 genomes]
rs4744430	0.83[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs4744431	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4744432	0.83[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs4744433	0.83[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs4744436	0.83[CEU][hapmap]
rs6479588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479591	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6479592	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7021351	0.90[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022452	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7023719	0.81[CHB][hapmap]
rs7043705	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7048786	0.90[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs7048941	0.90[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs7851173	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7857679	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7862156	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs7863291	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes]
rs7865144	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7873479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873567	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs962229	0.83[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4744422	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97765200-97770600	Active TSS	Aorta	Aorta
2	chr9:97765800-97770800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr9:97765800-97772600	Active TSS	Stomach Smooth Muscle	stomach
4	chr9:97766000-97770600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr9:97766000-97770600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr9:97766000-97770800	Active TSS	Colonic Mucosa	Colon
7	chr9:97766000-97771000	Active TSS	Colon Smooth Muscle	Colon
8	chr9:97766200-97770600	Active TSS	Brain Hippocampus Middle	brain
9	chr9:97766200-97771000	Active TSS	Right Ventricle	heart
10	chr9:97766200-97771200	Active TSS	Fetal Kidney	kidney
11	chr9:97766200-97771800	Active TSS	Right Atrium	heart
12	chr9:97766400-97771000	Active TSS	Brain Angular Gyrus	brain
13	chr9:97766400-97771000	Active TSS	Brain Cingulate Gyrus	brain
14	chr9:97766400-97771000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:97766400-97771000	Active TSS	Brain Substantia Nigra	brain
16	chr9:97766400-97771400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr9:97766600-97771000	Active TSS	Esophagus	oesophagus
18	chr9:97767800-97771200	Transcr. at gene 5' and 3'	HSMM	muscle
19	chr9:97767800-97771400	Transcr. at gene 5' and 3'	Osteobl	bone
20	chr9:97767800-97773600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:97767800-97775200	Transcr. at gene 5' and 3'	A549	lung
22	chr9:97768000-97771200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
23	chr9:97768000-97776400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:97768000-97781000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:97768000-97781000	Weak transcription	Gastric	stomach
26	chr9:97768000-97783800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:97768000-97786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:97768200-97779400	Weak transcription	Fetal Brain Female	brain
29	chr9:97768200-97779800	Weak transcription	K562	blood
30	chr9:97768400-97770800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr9:97768600-97771000	Flanking Active TSS	HMEC	breast
32	chr9:97768600-97771000	Transcr. at gene 5' and 3'	NH-A	brain
33	chr9:97768800-97770800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
34	chr9:97768800-97770800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
35	chr9:97768800-97771000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:97768800-97771000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:97768800-97771200	Transcr. at gene 5' and 3'	NHEK	skin
38	chr9:97768800-97781800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:97768800-97785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:97769000-97770600	Enhancers	Stomach Mucosa	stomach
41	chr9:97769000-97779400	Weak transcription	GM12878-XiMat	blood
42	chr9:97769000-97783800	Weak transcription	Fetal Brain Male	brain
43	chr9:97769000-97787600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:97769200-97772800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:97769600-97784200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:97769800-97770800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:97769800-97770800	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
49	chr9:97769800-97771000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:97769800-97771000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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