Variant report

Variant	rs3802456
Chromosome Location	chr9:97771852-97771853
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97771036..97773650-chr9:97778187..97780629,2	K562	blood:
2	chr9:97769757..97772435-chr9:97816536..97818768,2	K562	blood:
3	chr9:97534491..97536621-chr9:97770920..97772463,2	MCF-7	breast:
4	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
5	chr9:97563450..97566296-chr9:97770387..97772298,3	MCF-7	breast:
6	chr9:97769187..97771943-chr9:97834202..97836015,2	MCF-7	breast:
7	chr9:97543390..97547292-chr9:97769751..97772749,5	MCF-7	breast:
8	chr9:97634532..97637191-chr9:97769954..97772571,2	MCF-7	breast:
9	chr9:97770812..97773643-chr9:97773924..97776829,2	K562	blood:
10	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
11	chr9:97771150..97772727-chr9:97906869..97908913,2	MCF-7	breast:
12	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:
13	chr9:97769731..97772071-chr9:97808769..97812479,5	MCF-7	breast:
14	chr9:97723418..97725512-chr9:97771283..97773130,2	MCF-7	breast:
15	chr9:97399443..97401665-chr9:97771079..97774076,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction
ENSG00000207617	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1004373	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10117370	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10119512	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10121760	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10123819	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1020963	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10512253	0.83[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761366	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761368	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10761369	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs10993427	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10993435	0.83[CHB][hapmap]
rs10993449	0.83[CHB][hapmap]
rs10993464	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10993467	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1113102	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1412488	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1564234	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1571894	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1571895	0.91[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2061800	0.89[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2404295	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2404302	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2404305	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2404456	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2896816	0.83[CHB][hapmap]
rs3802454	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4537362	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4743979	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743980	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743981	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4743982	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743984	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744422	0.83[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744424	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744425	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744426	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744428	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4744430	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744431	0.83[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4744432	0.83[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4744433	0.83[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4744435	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744436	0.83[CEU][hapmap];0.88[AMR][1000 genomes]
rs6479588	0.83[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6479591	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6479592	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7020709	0.92[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7021351	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7022452	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7042271	0.81[CHB][hapmap]
rs7043705	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7048786	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7048941	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7851173	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7854831	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7857679	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7862156	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7863291	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7865144	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871218	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7873479	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7873567	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs962229	0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][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
rs3802456	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97765800-97772600	Active TSS	Stomach Smooth Muscle	stomach
2	chr9:97767800-97773600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:97767800-97775200	Transcr. at gene 5' and 3'	A549	lung
4	chr9:97768000-97776400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:97768000-97781000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:97768000-97781000	Weak transcription	Gastric	stomach
7	chr9:97768000-97783800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr9:97768000-97786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:97768200-97779400	Weak transcription	Fetal Brain Female	brain
10	chr9:97768200-97779800	Weak transcription	K562	blood
11	chr9:97768800-97781800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:97768800-97785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:97769000-97779400	Weak transcription	GM12878-XiMat	blood
14	chr9:97769000-97783800	Weak transcription	Fetal Brain Male	brain
15	chr9:97769000-97787600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:97769200-97772800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:97769600-97784200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:97770000-97772000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:97770000-97772000	Transcr. at gene 5' and 3'	HSMMtube	muscle
21	chr9:97770000-97781200	Weak transcription	Small Intestine	intestine
22	chr9:97770400-97774600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:97770600-97772000	Weak transcription	Stomach Mucosa	stomach
24	chr9:97770600-97773200	Strong transcription	Placenta	Placenta
25	chr9:97770600-97774200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:97770600-97780800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:97770800-97772600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:97770800-97772600	Weak transcription	Pancreas	Pancrea
29	chr9:97770800-97773800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:97770800-97777400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:97770800-97781600	Weak transcription	Colonic Mucosa	Colon
32	chr9:97770800-97782000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:97770800-97782200	Weak transcription	Lung	lung
34	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
35	chr9:97771000-97772600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:97771000-97772600	Weak transcription	Brain Angular Gyrus	brain
37	chr9:97771000-97772600	Enhancers	Brain Anterior Caudate	brain
38	chr9:97771000-97772600	Weak transcription	Brain Germinal Matrix	brain
39	chr9:97771000-97772600	Weak transcription	Fetal Muscle Leg	muscle
40	chr9:97771000-97772600	Weak transcription	Fetal Stomach	stomach
41	chr9:97771000-97772600	Weak transcription	Right Ventricle	heart
42	chr9:97771000-97772600	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr9:97771000-97772800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr9:97771000-97773200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:97771000-97773200	Genic enhancers	NH-A	brain
46	chr9:97771000-97773400	Enhancers	Fetal Heart	heart
47	chr9:97771000-97774200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:97771000-97775800	Enhancers	Brain Hippocampus Middle	brain
49	chr9:97771000-97777000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr9:97771000-97778200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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