Variant report

Variant	rs9496738
Chromosome Location	chr6:144020461-144020462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144018054..144020954-chr6:144022528..144024554,3	MCF-7	breast:
2	chr6:143831227..143833944-chr6:144017748..144020555,2	MCF-7	breast:
3	chr6:144020099..144020600-chr6:144334156..144334754,2	K562	blood:
4	chr6:144011387..144013559-chr6:144018568..144021455,2	MCF-7	breast:
5	chr6:144019071..144021984-chr6:144030527..144032678,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000001036	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11755709	0.84[ASN][1000 genomes]
rs12199447	0.84[ASN][1000 genomes]
rs12200809	0.80[ASN][1000 genomes]
rs12524982	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12525281	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12525974	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12527275	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530178	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192672	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13193972	0.84[ASN][1000 genomes]
rs13199178	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13213692	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13214196	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13219740	0.80[ASN][1000 genomes]
rs17291151	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1884172	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2051009	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34775537	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62427376	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62427377	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6932482	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9484795	0.84[EUR][1000 genomes]
rs9496740	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv886737	chr6:144010570-144033992	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144011600-144053200	Weak transcription	Hela-S3	cervix
2	chr6:144012200-144026800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:144014200-144027800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:144014200-144039800	Weak transcription	Pancreas	Pancrea
5	chr6:144014400-144022600	Weak transcription	Fetal Intestine Large	intestine
6	chr6:144014800-144020800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:144015400-144020800	Weak transcription	Lung	lung
8	chr6:144015400-144034600	Weak transcription	Esophagus	oesophagus
9	chr6:144015800-144021800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:144016000-144021800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:144016000-144022000	Weak transcription	HSMMtube	muscle
12	chr6:144016200-144021600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:144016200-144023000	Enhancers	Adipose Nuclei	Adipose
14	chr6:144016200-144037200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:144016200-144038000	Weak transcription	NHEK	skin
16	chr6:144016400-144022000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:144016600-144034000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:144016600-144034000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:144016800-144021800	Weak transcription	Brain Substantia Nigra	brain
20	chr6:144017000-144021000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:144017000-144022000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:144017000-144022200	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:144017000-144023000	Weak transcription	Fetal Intestine Small	intestine
24	chr6:144017000-144023200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:144017000-144026800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:144017000-144038200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:144017200-144044200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:144017400-144021600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:144017400-144021800	Weak transcription	Small Intestine	intestine
30	chr6:144017400-144034400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:144017600-144026800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:144017800-144047200	Weak transcription	K562	blood
33	chr6:144018000-144022200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:144018000-144030800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:144018200-144021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:144018200-144021800	Weak transcription	NHLF	lung
37	chr6:144018200-144022000	Weak transcription	Fetal Heart	heart
38	chr6:144018200-144023000	Weak transcription	Aorta	Aorta
39	chr6:144018200-144026800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:144018200-144044400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:144018600-144021800	Weak transcription	Stomach Mucosa	stomach
42	chr6:144018600-144030600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr6:144018800-144020600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:144018800-144020600	Weak transcription	Fetal Kidney	kidney
45	chr6:144019000-144021800	Weak transcription	NH-A	brain
46	chr6:144019000-144022200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:144019000-144028800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:144019200-144021600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:144019200-144023200	Enhancers	HUVEC	blood vessel
50	chr6:144019200-144023800	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links