Variant report

Variant	rs34683820
Chromosome Location	chr3:42647769-42647770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42647403..42649069-chr3:42694170..42697122,2	K562	blood:
2	chr3:42632973..42636724-chr3:42645956..42649361,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230084	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1062051	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085695	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13089845	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090902	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13093680	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095447	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17074662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074664	0.89[ASN][1000 genomes]
rs17074669	0.89[ASN][1000 genomes]
rs17074673	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074674	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074680	0.89[ASN][1000 genomes]
rs17074693	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284303	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284304	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300057	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300058	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302352	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33969824	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33984028	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34687113	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34762478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34801786	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34852409	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34977988	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35506005	0.82[ASN][1000 genomes]
rs35676838	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35770315	0.89[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36033201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774402	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774404	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774406	0.82[ASN][1000 genomes]
rs3774407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846058	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3846059	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856737	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886782	0.82[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs56797870	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57259216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59914338	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60232916	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60348477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66786953	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67059259	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67165547	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.81[ASN][1000 genomes]
rs6778982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782164	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	0.81[EUR][1000 genomes]
rs6793186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795296	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797491	0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68071013	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72864072	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7617403	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617736	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643000-42650000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:42643000-42650000	Weak transcription	Esophagus	oesophagus
3	chr3:42643200-42648400	Weak transcription	Placenta	Placenta
4	chr3:42643200-42649600	Weak transcription	Lung	lung
5	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:42643400-42647800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:42643600-42648400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
9	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:42644000-42648200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:42644000-42648400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:42644000-42649800	Weak transcription	Right Atrium	heart
13	chr3:42644000-42660000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
17	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:42644200-42648000	Weak transcription	Fetal Intestine Large	intestine
19	chr3:42644200-42648400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:42644200-42648400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:42644200-42648400	Weak transcription	Thymus	Thymus
22	chr3:42644200-42649800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:42644200-42649800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:42644200-42655200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:42644200-42663200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
27	chr3:42644400-42653600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:42644800-42648200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:42644800-42649600	Weak transcription	Left Ventricle	heart
30	chr3:42644800-42649600	Weak transcription	Ovary	ovary
31	chr3:42644800-42649800	Weak transcription	Small Intestine	intestine
32	chr3:42644800-42650200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:42644800-42660000	Weak transcription	Colonic Mucosa	Colon
34	chr3:42644800-42660200	Weak transcription	NH-A	brain
35	chr3:42645000-42649400	Strong transcription	Primary B cells from cord blood	blood
36	chr3:42645200-42648400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:42645200-42652200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:42645200-42660200	Weak transcription	HMEC	breast
39	chr3:42645600-42648600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:42645600-42649400	Weak transcription	Fetal Stomach	stomach
41	chr3:42645600-42650400	Strong transcription	Fetal Thymus	thymus
42	chr3:42645600-42653400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:42645800-42649800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:42646000-42648400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:42646000-42648400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:42646000-42648400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:42646000-42648800	Strong transcription	Fetal Lung	lung
48	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:42646200-42648000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:42646200-42648000	Enhancers	HepG2	liver

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