Variant report

Variant	rs334561
Chromosome Location	chr3:119784996-119784997
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119779724..119782667-chr3:119783390..119785104,2	MCF-7	breast:
2	chr3:119783496..119785978-chr3:119811457..119815563,3	K562	blood:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10049256	0.88[CEU][hapmap]
rs10934512	0.87[CEU][hapmap]
rs1154596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1154597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11921053	0.91[ASN][1000 genomes]
rs12152218	0.88[CEU][hapmap]
rs13312998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13314595	1.00[CHB][hapmap]
rs1488764	0.87[CEU][hapmap]
rs1626696	0.83[EUR][1000 genomes]
rs16830683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830689	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1719888	0.87[AFR][1000 genomes]
rs1719895	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1732165	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1732169	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs182839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs184576	0.87[EUR][1000 genomes]
rs1907681	0.88[CEU][hapmap]
rs2035671	0.88[CEU][hapmap]
rs2035674	0.87[CEU][hapmap]
rs2130000	0.88[CEU][hapmap]
rs2319541	0.88[CEU][hapmap]
rs2319543	0.88[CEU][hapmap]
rs2461827	0.82[ASN][1000 genomes]
rs2874022	0.85[CEU][hapmap]
rs2874023	0.88[CEU][hapmap]
rs3108749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112282	0.84[AMR][1000 genomes]
rs3112283	0.84[AMR][1000 genomes]
rs334534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334535	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs334536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334539	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs334540	0.87[AMR][1000 genomes]
rs334545	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs334549	0.87[CEU][hapmap];0.84[AMR][1000 genomes]
rs334551	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs334552	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334554	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334559	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs334560	0.97[ASN][1000 genomes]
rs334565	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs334566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3853592	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4072520	1.00[CHB][hapmap]
rs4438691	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4488869	0.87[CEU][hapmap]
rs4605584	0.83[EUR][1000 genomes]
rs4676822	0.88[CEU][hapmap]
rs4688043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60272712	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6438558	0.87[CEU][hapmap]
rs6438559	0.87[CEU][hapmap]
rs6438564	0.87[CEU][hapmap]
rs6438567	0.88[CEU][hapmap]
rs66650215	0.88[ASN][1000 genomes]
rs6762640	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764549	0.88[CEU][hapmap]
rs6764558	0.92[AFR][1000 genomes]
rs6769435	1.00[CHB][hapmap]
rs6769988	0.88[CEU][hapmap]
rs6770314	1.00[CHB][hapmap]
rs6771023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6774693	0.91[ASN][1000 genomes]
rs6776122	0.88[CEU][hapmap]
rs6779828	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6781470	0.87[CEU][hapmap]
rs6784239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6785050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6794478	0.85[CEU][hapmap]
rs6797689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6802301	0.81[ASN][1000 genomes]
rs6805931	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7617372	1.00[CHB][hapmap]
rs7620750	0.82[CHB][hapmap]
rs7624540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7628426	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7635604	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636600	0.91[ASN][1000 genomes]
rs7644268	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs7650554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7652172	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7653263	0.87[CEU][hapmap]
rs7653396	0.85[CEU][hapmap]
rs902790	0.87[CEU][hapmap]
rs902791	0.88[CEU][hapmap]
rs902794	0.88[CEU][hapmap]
rs902795	0.88[CEU][hapmap]
rs923380	0.87[CEU][hapmap]
rs923726	0.88[CEU][hapmap]
rs923727	0.88[CEU][hapmap]
rs923728	0.87[CEU][hapmap]
rs9289143	0.87[CEU][hapmap]
rs968824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs979682	0.87[CEU][hapmap]
rs9813834	0.88[CEU][hapmap]
rs9829763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9842302	0.87[CEU][hapmap]
rs9851174	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9853082	0.87[CEU][hapmap]
rs9858566	0.88[CEU][hapmap]
rs9859778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9879992	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119759400-119786200	Weak transcription	Hela-S3	cervix
2	chr3:119760200-119805400	Weak transcription	HMEC	breast
3	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119768800-119792800	Weak transcription	Fetal Stomach	stomach
5	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:119771800-119805400	Weak transcription	NHEK	skin
8	chr3:119773200-119807600	Weak transcription	Right Ventricle	heart
9	chr3:119773800-119787800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:119774000-119789600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:119775800-119790400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:119775800-119796000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:119775800-119797600	Weak transcription	Fetal Thymus	thymus
14	chr3:119778600-119786400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:119778800-119786000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:119778800-119787800	Weak transcription	Primary B cells from cord blood	blood
17	chr3:119778800-119791200	Weak transcription	Fetal Brain Female	brain
18	chr3:119778800-119796000	Weak transcription	NHDF-Ad	bronchial
19	chr3:119778800-119796400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:119779000-119788200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:119779200-119789200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:119779200-119789200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:119779200-119789200	Weak transcription	A549	lung
24	chr3:119779400-119789200	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:119779400-119804200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:119779400-119807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:119779600-119786400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:119779600-119787800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:119779600-119789200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:119779600-119789600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:119779600-119789800	Weak transcription	Small Intestine	intestine
32	chr3:119779600-119793000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:119779600-119800200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:119779600-119807800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:119779800-119786200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:119779800-119793000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:119780000-119786400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:119780000-119788200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:119780400-119785400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:119780600-119807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:119781800-119788000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:119782000-119789800	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:119782800-119790200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:119783400-119785200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:119783400-119786200	Weak transcription	Adipose Nuclei	Adipose
46	chr3:119783600-119785200	ZNF genes & repeats	GM12878-XiMat	blood
47	chr3:119783600-119789600	Weak transcription	HepG2	liver
48	chr3:119783800-119789200	Weak transcription	Brain Anterior Caudate	brain
49	chr3:119784000-119785000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:119784400-119785200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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