Variant report

Variant	rs9496336
Chromosome Location	chr6:142645736-142645737
allele	C/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	chr6:142644270..142645921-chr6:142696254..142697871,2	MCF-7	breast:
5	chr6:142622670..142624423-chr6:142644987..142647948,3	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: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13437156	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1411147	1.00[AMR][1000 genomes]
rs6921559	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484627	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484629	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484634	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484635	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484636	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484638	1.00[AMR][1000 genomes]
rs9484640	1.00[AMR][1000 genomes]
rs9484641	1.00[AMR][1000 genomes]
rs9484644	1.00[AMR][1000 genomes]
rs9496350	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496351	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496359	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496362	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496363	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496375	1.00[AMR][1000 genomes]
rs9496376	1.00[AMR][1000 genomes]
rs9496381	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496383	1.00[AMR][1000 genomes]
rs9496384	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496385	1.00[AMR][1000 genomes]
rs9496386	1.00[AMR][1000 genomes]
rs9496387	1.00[AMR][1000 genomes]
rs9496393	1.00[AMR][1000 genomes]
rs9496407	1.00[AMR][1000 genomes]
rs9496408	1.00[AMR][1000 genomes]
rs9496410	1.00[AMR][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:29 , 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	chr6:142644000-142646400	Enhancers	Stomach Mucosa	stomach
12	chr6:142644000-142646600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:142644200-142646000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr6:142644200-142646400	Genic enhancers	HepG2	liver
15	chr6:142644400-142645800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr6:142644600-142646400	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr6:142644600-142646400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:142645000-142645800	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr6:142645000-142646000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:142645000-142646600	Enhancers	Fetal Intestine Large	intestine
21	chr6:142645000-142646600	Enhancers	Fetal Intestine Small	intestine
22	chr6:142645200-142645800	Enhancers	H9 Cell Line	embryonic stem cell
23	chr6:142645200-142647800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:142645400-142646200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:142645400-142647800	Weak transcription	Liver	Liver
26	chr6:142645400-142650200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:142645400-142650600	Weak transcription	HMEC	breast
28	chr6:142645600-142645800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr6:142645600-142646600	Flanking Active TSS	A549	lung

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