Variant report

Variant	rs3769213
Chromosome Location	chr2:173910787-173910788
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173908637..173910994-chr2:174830078..174831720,2	MCF-7	breast:
2	chr2:173885808..173888407-chr2:173907815..173910951,3	MCF-7	breast:
3	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:
4	chr2:173903690..173905721-chr2:173909979..173911933,2	K562	blood:
5	chr2:173895149..173898676-chr2:173907706..173911844,6	MCF-7	breast:
6	chr2:173905270..173911343-chr2:173911871..173916630,12	MCF-7	breast:
7	chr2:173909580..173911400-chr2:173932850..173935097,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172845	Chromatin interaction
ENSG00000091436	Chromatin interaction
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1020599	0.94[CEU][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10497403	0.94[CEU][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11687539	0.83[CEU][hapmap]
rs12463612	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs12464956	0.88[ASW][hapmap];0.94[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12474338	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474484	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1551248	0.84[CEU][hapmap];0.84[ASN][1000 genomes]
rs1551249	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17710437	0.82[CEU][hapmap]
rs1973037	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012213	0.94[ASW][hapmap];0.84[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3754747	0.83[CEU][hapmap]
rs3769201	0.82[CHD][hapmap]
rs3769210	0.84[CEU][hapmap]
rs3769211	0.84[CEU][hapmap]
rs3820835	0.82[CEU][hapmap]
rs4972529	0.82[CEU][hapmap]
rs60121307	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6717489	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6717529	1.00[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6717735	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6742219	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs734993	0.82[CEU][hapmap]
rs746179	0.83[CEU][hapmap]

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	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3769213	ZAK	Cis_1M	lymphoblastoid	RTeQTL
rs3769213	CYBRD1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173881200-173912800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:173893000-173913200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:173893200-173922000	Weak transcription	Brain Anterior Caudate	brain
4	chr2:173901000-173918000	Weak transcription	Brain Angular Gyrus	brain
5	chr2:173904400-173921400	Weak transcription	Ovary	ovary
6	chr2:173904600-173913000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:173906800-173912800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:173906800-173913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:173908600-173916800	Enhancers	Fetal Intestine Large	intestine
10	chr2:173908600-173921400	Weak transcription	Left Ventricle	heart
11	chr2:173908800-173911200	Weak transcription	Fetal Heart	heart
12	chr2:173908800-173912800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:173908800-173912800	Weak transcription	Stomach Mucosa	stomach
14	chr2:173908800-173914400	Weak transcription	Liver	Liver
15	chr2:173908800-173924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:173909000-173912800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:173909000-173916800	Enhancers	Fetal Intestine Small	intestine
18	chr2:173909400-173912800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:173909600-173912800	Enhancers	A549	lung
20	chr2:173909800-173912200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:173909800-173915000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:173909800-173915200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:173910000-173912600	Weak transcription	HMEC	breast
24	chr2:173910000-173912800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:173910200-173910800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:173910200-173911600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:173910200-173913000	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:173910400-173910800	Enhancers	Small Intestine	intestine
29	chr2:173910400-173913000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:173910600-173910800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:173910600-173910800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:173910600-173912600	Weak transcription	NHLF	lung
33	chr2:173910600-173913000	Weak transcription	Fetal Lung	lung
34	chr2:173910600-173913000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:173910600-173913200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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