Variant report

Variant	rs334554
Chromosome Location	chr3:119802373-119802374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1154596	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1154597	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11921053	0.94[ASN][1000 genomes]
rs13312998	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16830683	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830689	0.84[ASN][1000 genomes]
rs1719895	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732165	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732169	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs182839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184576	0.85[EUR][1000 genomes]
rs2461827	0.85[ASN][1000 genomes]
rs3108749	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3112282	0.84[AMR][1000 genomes]
rs3112283	0.84[AMR][1000 genomes]
rs334534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334535	0.84[ASN][1000 genomes]
rs334536	1.00[ASN][1000 genomes]
rs334539	0.87[AMR][1000 genomes]
rs334540	0.87[AMR][1000 genomes]
rs334545	0.87[AMR][1000 genomes]
rs334549	0.84[AMR][1000 genomes]
rs334551	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334559	0.84[ASN][1000 genomes]
rs334560	1.00[ASN][1000 genomes]
rs334561	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334566	1.00[ASN][1000 genomes]
rs3853592	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4438691	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688043	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60272712	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438554	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438555	1.00[ASN][1000 genomes]
rs66650215	0.91[ASN][1000 genomes]
rs6762640	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771023	0.94[ASN][1000 genomes]
rs6774693	0.94[ASN][1000 genomes]
rs6779828	0.84[ASN][1000 genomes]
rs6784239	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785050	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6797689	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802301	0.84[ASN][1000 genomes]
rs6805931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807868	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624540	0.85[ASN][1000 genomes]
rs7628426	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635604	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7636600	0.94[ASN][1000 genomes]
rs7644268	0.84[AMR][1000 genomes]
rs7650554	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652172	0.84[ASN][1000 genomes]
rs968824	1.00[ASN][1000 genomes]
rs9851174	0.84[ASN][1000 genomes]
rs9859778	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119760200-119805400	Weak transcription	HMEC	breast
2	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:119771800-119805400	Weak transcription	NHEK	skin
6	chr3:119773200-119807600	Weak transcription	Right Ventricle	heart
7	chr3:119779400-119804200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:119779400-119807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:119779600-119807800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:119780600-119807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:119788400-119805400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:119788400-119808600	Weak transcription	Primary B cells from cord blood	blood
13	chr3:119789400-119809200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:119789800-119807800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:119790000-119807600	Weak transcription	Liver	Liver
16	chr3:119790200-119805000	Weak transcription	HepG2	liver
17	chr3:119790400-119805200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:119790600-119807400	Weak transcription	Brain Substantia Nigra	brain
19	chr3:119790600-119807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:119790600-119809200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:119790800-119808000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:119790800-119809200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:119790800-119809400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:119791000-119809600	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:119793000-119807400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:119793200-119805400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:119795200-119805200	Weak transcription	Hela-S3	cervix
28	chr3:119796400-119802400	Weak transcription	Fetal Heart	heart
29	chr3:119796400-119804800	Weak transcription	Stomach Mucosa	stomach
30	chr3:119796600-119802400	Weak transcription	Adipose Nuclei	Adipose
31	chr3:119796600-119804600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:119796800-119806000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:119797000-119807400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:119797000-119807800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:119797200-119807600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:119797600-119808000	Weak transcription	NHLF	lung
37	chr3:119797800-119804400	Weak transcription	Fetal Brain Male	brain
38	chr3:119797800-119805200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:119798000-119805400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:119798000-119807600	Weak transcription	NHDF-Ad	bronchial
41	chr3:119798400-119807600	Weak transcription	Right Atrium	heart
42	chr3:119798400-119809400	Weak transcription	Lung	lung
43	chr3:119798600-119804400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:119798600-119807400	Weak transcription	Thymus	Thymus
45	chr3:119798600-119807600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:119798600-119807600	Weak transcription	Fetal Thymus	thymus
47	chr3:119798800-119807600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:119798800-119807800	Weak transcription	K562	blood
49	chr3:119799000-119807600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:119799000-119808000	Weak transcription	Primary hematopoietic stem cells	blood

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