Variant report

Variant	rs9403379
Chromosome Location	chr6:142644881-142644882
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142644594..142647193-chr6:142697392..142699700,4	MCF-7	breast:
2	chr6:142644240..142648928-chr6:142651290..142656139,5	MCF-7	breast:
3	chr6:142638506..142640750-chr6:142643071..142645808,2	MCF-7	breast:
4	chr6:142642940..142645383-chr6:142647071..142650024,3	MCF-7	breast:
5	chr6:142644270..142645921-chr6:142696254..142697871,2	MCF-7	breast:
6	chr6:142643388..142647165-chr6:142648563..142652325,5	MCF-7	breast:
7	chr6:142621728..142625423-chr6:142644550..142646959,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1013902	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17071798	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2064314	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2143390	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2223616	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294765	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294768	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294770	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2294772	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294773	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294774	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34701089	0.81[EUR][1000 genomes]
rs41289839	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4140531	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6570512	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6913116	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7758750	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7759268	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9321865	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373343	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373345	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9376687	1.00[EUR][1000 genomes]
rs9376689	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9385993	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385994	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9389988	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9389990	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403384	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9484645	0.81[EUR][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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142624800-142651800	Weak transcription	HSMM	muscle
2	chr6:142626000-142650600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:142633200-142651000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:142634800-142646400	Weak transcription	HUVEC	blood vessel
5	chr6:142635000-142651000	Weak transcription	NHEK	skin
6	chr6:142640400-142649800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:142640400-142652000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:142640600-142651200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:142642600-142646400	Enhancers	Fetal Lung	lung
10	chr6:142643000-142653800	Weak transcription	Fetal Heart	heart
11	chr6:142643600-142645000	Weak transcription	Fetal Intestine Large	intestine
12	chr6:142644000-142645000	Flanking Active TSS	A549	lung
13	chr6:142644000-142646400	Enhancers	Stomach Mucosa	stomach
14	chr6:142644000-142646600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:142644200-142645400	Enhancers	HMEC	breast
16	chr6:142644200-142646000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr6:142644200-142646400	Genic enhancers	HepG2	liver
18	chr6:142644400-142645800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:142644600-142645000	Enhancers	H9 Cell Line	embryonic stem cell
20	chr6:142644600-142645200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:142644600-142645400	Enhancers	Liver	Liver
22	chr6:142644600-142645600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:142644600-142646400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr6:142644600-142646400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:142644800-142645200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr6:142644800-142645400	Enhancers	HUES64 Cell Line	embryonic stem cell

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