Variant report

Variant	rs9859641
Chromosome Location	chr3:160964811-160964812
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160963016..160968283-chr3:161087756..161091346,7	MCF-7	breast:
2	chr3:160956099..160961317-chr3:160961958..160964988,5	K562	blood:
3	chr3:160948054..160951882-chr3:160963118..160966934,5	K562	blood:
4	chr3:160963270..160965103-chr3:161124970..161126764,2	MCF-7	breast:
5	chr3:160962204..160965974-chr3:160967847..160971324,6	MCF-7	breast:
6	chr3:160945707..160948302-chr3:160963989..160965860,2	K562	blood:
7	chr3:160959557..160961368-chr3:160962963..160965074,2	MCF-7	breast:
8	chr3:160964409..160966384-chr3:161129795..161132024,2	MCF-7	breast:
9	chr3:160962510..160966697-chr3:161085167..161089151,3	MCF-7	breast:
10	chr3:160963417..160965980-chr3:160971086..160973267,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1017799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12486069	0.87[ASN][1000 genomes]
rs12486111	0.88[JPT][hapmap]
rs12486998	0.88[JPT][hapmap]
rs12487002	0.89[JPT][hapmap]
rs12488127	0.88[JPT][hapmap]
rs12489004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12489125	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12490149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494725	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12496235	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13315320	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13319558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13319771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1450518	0.86[JPT][hapmap]
rs16831799	0.85[AMR][1000 genomes]
rs16831850	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831864	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831882	0.87[ASN][1000 genomes]
rs16831942	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2306209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28451189	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28704960	0.87[ASN][1000 genomes]
rs28713364	0.97[AMR][1000 genomes]
rs3925722	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4296611	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4352387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4468992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4580574	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4635725	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57903480	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59567999	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59593286	0.83[AMR][1000 genomes]
rs59757775	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59776766	0.87[ASN][1000 genomes]
rs59867530	0.82[AMR][1000 genomes]
rs60121330	0.87[ASN][1000 genomes]
rs6441350	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6441363	0.94[AMR][1000 genomes]
rs6441365	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6441372	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6762064	0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6771581	0.83[AMR][1000 genomes]
rs6774919	0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6775446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6775931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6778186	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6782415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6782518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6785714	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6787447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6788738	0.97[AMR][1000 genomes]
rs6790805	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6794601	0.88[JPT][hapmap]
rs6796168	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6801664	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805976	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73017340	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026933	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026967	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026968	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026983	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026987	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026989	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73878309	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7615833	1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7615868	0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7624791	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7626773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7634299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7651924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7652624	0.82[CHB][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9290070	0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9290071	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9682249	0.85[AMR][1000 genomes]
rs9810351	0.87[ASN][1000 genomes]
rs9812574	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9818470	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818835	0.87[ASN][1000 genomes]
rs9818992	0.82[ASN][1000 genomes]
rs9819793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822705	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9822916	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9823424	0.87[ASN][1000 genomes]
rs9824535	0.87[ASN][1000 genomes]
rs9824805	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826857	0.87[ASN][1000 genomes]
rs9830183	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9833270	0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9834806	0.94[AMR][1000 genomes]
rs9835530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9838945	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9841871	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9842290	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9847842	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9850455	0.89[JPT][hapmap]
rs9851699	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855112	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855572	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9856742	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858907	0.87[ASN][1000 genomes]
rs9860980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9862867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9871753	0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9872514	0.89[JPT][hapmap]
rs9876077	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9877309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9884100	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9985364	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 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	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160940000-160971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160940200-160965400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:160941000-160969600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:160941000-160970200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:160941000-160974800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
9	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
10	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
11	chr3:160941200-160968600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:160941200-160969800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:160941200-160973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:160941400-160971800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:160941600-160969800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:160941600-160975400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:160941800-160975200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:160942200-160973200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:160942400-160975200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:160942600-160965400	Weak transcription	Gastric	stomach
21	chr3:160942600-160971800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:160942600-160972600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:160942600-160973400	Strong transcription	Fetal Thymus	thymus
24	chr3:160942600-160975000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:160942600-160976600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:160942800-160971800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:160942800-160973800	Strong transcription	NH-A	brain
28	chr3:160942800-160978000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:160943000-160965400	Weak transcription	Right Ventricle	heart
30	chr3:160943600-160977200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:160945600-160965200	Weak transcription	Fetal Intestine Small	intestine
32	chr3:160946400-160972800	Strong transcription	HSMM	muscle
33	chr3:160947000-160965800	Weak transcription	Brain Angular Gyrus	brain
34	chr3:160947200-160972600	Weak transcription	Stomach Mucosa	stomach
35	chr3:160947400-160967600	Weak transcription	Fetal Brain Male	brain
36	chr3:160947400-160973600	Strong transcription	HUVEC	blood vessel
37	chr3:160947600-160967000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:160948000-160965000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:160948800-160965400	Weak transcription	Thymus	Thymus
40	chr3:160948800-160971600	Weak transcription	Aorta	Aorta
41	chr3:160948800-160978000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:160949200-160971200	Weak transcription	Brain Substantia Nigra	brain
43	chr3:160949800-160971200	Weak transcription	Fetal Heart	heart
44	chr3:160950000-160969600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:160950000-160978000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:160950200-160968600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:160950200-160976600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:160950600-160972800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:160950800-160967600	Weak transcription	Fetal Brain Female	brain
50	chr3:160950800-160971200	Strong transcription	NHDF-Ad	bronchial

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