Variant report

Variant	rs41408445
Chromosome Location	chr6:36815891-36815892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36813097..36817689-chr6:36839602..36844147,5	K562	blood:
2	chr6:36811002..36813494-chr6:36814165..36817730,3	MCF-7	breast:
3	chr6:36562562..36564924-chr6:36814453..36817314,2	K562	blood:
4	chr6:36813865..36816350-chr6:36831704..36833513,2	MCF-7	breast:
5	chr6:36815094..36818441-chr6:36826786..36830432,3	K562	blood:
6	chr6:36808554..36811671-chr6:36814361..36817752,3	MCF-7	breast:
7	chr6:36815130..36818530-chr6:36818954..36823604,5	K562	blood:
8	chr6:36802135..36806247-chr6:36814930..36817365,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137168	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10456445	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10456448	0.82[ASN][1000 genomes]
rs10947646	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs11964396	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111266	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111291	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12193721	0.82[ASN][1000 genomes]
rs12195012	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12215873	0.90[ASN][1000 genomes]
rs12524018	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524422	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs12524649	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12525540	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs12526699	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12529199	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12529769	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17374068	0.85[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs17552561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1864753	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35694858	0.88[AMR][1000 genomes]
rs41272192	0.90[ASN][1000 genomes]
rs4348312	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714013	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs4714022	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681762	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55913388	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55928881	0.82[ASN][1000 genomes]
rs56240344	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56302344	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66474948	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66566790	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67273613	0.88[EUR][1000 genomes]
rs68042914	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72846046	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72846078	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73416282	0.80[AMR][1000 genomes]
rs7745555	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762601	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41408445	C6orf89	cis	parietal	SCAN
rs41408445	PNPLA1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36808600-36818800	Weak transcription	Dnd41	blood
2	chr6:36808800-36816000	Weak transcription	Spleen	Spleen
3	chr6:36808800-36816600	Weak transcription	Aorta	Aorta
4	chr6:36809000-36816600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:36809000-36818600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:36809000-36820200	Weak transcription	Thymus	Thymus
7	chr6:36809000-36823000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:36809200-36816000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:36809200-36817000	Weak transcription	Brain Anterior Caudate	brain
10	chr6:36809200-36818000	Weak transcription	HSMM	muscle
11	chr6:36809200-36819200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:36809800-36818400	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:36811000-36816000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:36811000-36816000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:36811400-36823200	Weak transcription	Esophagus	oesophagus
16	chr6:36811600-36816200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:36812600-36816400	Weak transcription	Brain Germinal Matrix	brain
18	chr6:36812800-36816000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:36813200-36816400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:36813200-36821200	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:36813200-36823200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:36814000-36816200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:36814200-36817600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:36814800-36816200	Enhancers	K562	blood
25	chr6:36815000-36816400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:36815000-36816600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:36815200-36819200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:36815400-36816000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:36815400-36816200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:36815400-36816600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:36815400-36816600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:36815400-36816600	Enhancers	Duodenum Mucosa	Duodenum
33	chr6:36815400-36816600	Active TSS	Right Atrium	heart
34	chr6:36815400-36816800	Enhancers	Right Ventricle	heart
35	chr6:36815400-36817000	Enhancers	Left Ventricle	heart
36	chr6:36815400-36819800	Enhancers	Fetal Muscle Leg	muscle
37	chr6:36815600-36816000	Enhancers	Fetal Heart	heart
38	chr6:36815600-36816600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:36815600-36818400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:36815600-36819800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr6:36815800-36816000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
42	chr6:36815800-36816600	Enhancers	Gastric	stomach
43	chr6:36815800-36817000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr6:36815800-36817200	Enhancers	Stomach Mucosa	stomach
45	chr6:36815800-36817600	Enhancers	Fetal Intestine Large	intestine

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