Variant report

Variant	rs1973037
Chromosome Location	chr2:173909996-173909997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:173909223-173910077	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr2:173908986-173910048	MCF-7	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:173908637..173910994-chr2:174830078..174831720,2	MCF-7	breast:
2	chr2:173903027..173904652-chr2:173908089..173910075,2	MCF-7	breast:
3	chr2:173908929..173910664-chr2:173926220..173928176,2	K562	blood:
4	chr2:173885808..173888407-chr2:173907815..173910951,3	MCF-7	breast:
5	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:
6	chr13:29291574..29294456-chr2:173907850..173910644,2	MCF-7	breast:
7	chr2:173903690..173905721-chr2:173909979..173911933,2	K562	blood:
8	chr2:173895149..173898676-chr2:173907706..173911844,6	MCF-7	breast:
9	chr2:173905270..173911343-chr2:173911871..173916630,12	MCF-7	breast:
10	chr2:173909580..173911400-chr2:173932850..173935097,2	MCF-7	breast:
11	chr2:173907933..173910689-chr2:173917476..173919133,2	K562	blood:

No data

Variant related genes	Relation type
RAPGEF4	TF binding region
ENSG00000139508	Chromatin interaction
ENSG00000091428	Chromatin interaction
ENSG00000091436	Chromatin interaction
ENSG00000172845	Chromatin interaction
ENSG00000265709	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1020599	0.94[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10497403	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11687539	0.83[CEU][hapmap]
rs12463612	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs12464956	0.88[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12474338	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12474484	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1551248	0.84[CEU][hapmap];0.82[ASN][1000 genomes]
rs1551249	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17710437	0.82[CEU][hapmap]
rs2012213	0.94[ASW][hapmap];0.84[CEU][hapmap];0.82[CHD][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3754747	0.83[CEU][hapmap]
rs3769201	0.84[CHD][hapmap]
rs3769210	0.84[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs3769211	0.84[CEU][hapmap]
rs3769213	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]
rs3820835	0.82[CEU][hapmap]
rs4972529	0.82[CEU][hapmap]
rs60121307	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6717489	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6717529	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6717735	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6742219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1973037	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 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	chr2:173906400-173910200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:173906800-173912800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:173906800-173913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:173907600-173910400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:173907800-173910400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:173908000-173910600	Enhancers	Rectal Smooth Muscle	rectum
13	chr2:173908200-173910000	Enhancers	HMEC	breast
14	chr2:173908400-173910000	Enhancers	Placenta	Placenta
15	chr2:173908400-173910600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:173908400-173910600	Enhancers	NHLF	lung
17	chr2:173908600-173910000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr2:173908600-173916800	Enhancers	Fetal Intestine Large	intestine
19	chr2:173908600-173921400	Weak transcription	Left Ventricle	heart
20	chr2:173908800-173911200	Weak transcription	Fetal Heart	heart
21	chr2:173908800-173912800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:173908800-173912800	Weak transcription	Stomach Mucosa	stomach
23	chr2:173908800-173914400	Weak transcription	Liver	Liver
24	chr2:173908800-173924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:173909000-173912800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:173909000-173916800	Enhancers	Fetal Intestine Small	intestine
27	chr2:173909200-173910000	Enhancers	H9 Cell Line	embryonic stem cell
28	chr2:173909200-173910200	Enhancers	Colon Smooth Muscle	Colon
29	chr2:173909200-173910400	Enhancers	Fetal Stomach	stomach
30	chr2:173909200-173910600	Enhancers	Fetal Lung	lung
31	chr2:173909400-173912800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:173909600-173910000	Enhancers	Duodenum Mucosa	Duodenum
33	chr2:173909600-173912800	Enhancers	A549	lung
34	chr2:173909800-173910000	Enhancers	Stomach Smooth Muscle	stomach
35	chr2:173909800-173910200	Weak transcription	Pancreas	Pancrea
36	chr2:173909800-173910400	Weak transcription	Small Intestine	intestine
37	chr2:173909800-173910600	Enhancers	Fetal Kidney	kidney
38	chr2:173909800-173912200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:173909800-173915000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:173909800-173915200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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