Variant report

Variant	rs9462399
Chromosome Location	chr6:38141322-38141323
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38140845..38143617-chr6:38230207..38231726,2	MCF-7	breast:
2	chr6:38129827..38133473-chr6:38138909..38141756,3	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10456461	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10456462	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10947710	0.85[CEU][hapmap]
rs10947715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11750950	0.86[CEU][hapmap]
rs11751094	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11751153	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11751630	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752623	1.00[CHB][hapmap]
rs11753054	0.86[CEU][hapmap]
rs11753563	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11754980	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11755439	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11755600	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11756301	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs11756626	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11756902	0.86[CEU][hapmap]
rs11757072	0.92[CEU][hapmap]
rs11757654	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11758095	0.86[CEU][hapmap]
rs11758540	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11759483	0.86[CEU][hapmap]
rs11759816	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs12202202	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12202872	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12215376	1.00[ASN][1000 genomes]
rs12661480	0.86[CEU][hapmap]
rs12664900	0.86[CEU][hapmap]
rs17757975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[ASN][1000 genomes]
rs1923280	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1931760	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs1931761	1.00[CHB][hapmap]
rs2395692	0.86[CEU][hapmap]
rs2395693	0.86[CEU][hapmap]
rs3800364	0.86[CEU][hapmap]
rs4336442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56064162	1.00[ASN][1000 genomes]
rs72849815	1.00[ASN][1000 genomes]
rs72849852	1.00[ASN][1000 genomes]
rs752110	0.86[CEU][hapmap]
rs7748392	0.86[CEU][hapmap]
rs876818	0.86[CEU][hapmap]
rs9369034	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9462403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs9470765	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9470772	0.86[CEU][hapmap]
rs9470777	0.86[CEU][hapmap]
rs9470779	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9470784	0.86[CEU][hapmap]
rs9470794	0.85[CEU][hapmap]
rs9470798	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv524213	chr6:38106844-38160627	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv517973	chr6:38131442-38152460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
9	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers 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	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9462399	C6orf222	cis	cerebellum	SCAN
rs9462399	GDF5	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38091400-38141800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:38121000-38159600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:38121800-38153600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:38123200-38153200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:38123400-38155400	Weak transcription	Aorta	Aorta
6	chr6:38123400-38157000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:38123400-38176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:38123600-38144200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:38123600-38153000	Weak transcription	Primary B cells from cord blood	blood
10	chr6:38123800-38141400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:38123800-38151200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:38124000-38152200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:38124200-38151800	Weak transcription	Brain Anterior Caudate	brain
14	chr6:38124400-38144200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:38129200-38145600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:38129400-38144600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:38130000-38144400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:38131200-38143800	Weak transcription	Thymus	Thymus
19	chr6:38131800-38167800	Weak transcription	Right Atrium	heart
20	chr6:38133600-38144600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:38133600-38160400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:38133600-38164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:38136000-38159800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:38136800-38145200	Genic enhancers	Fetal Intestine Small	intestine
25	chr6:38136800-38156000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:38137200-38143000	Enhancers	Fetal Intestine Large	intestine
27	chr6:38137600-38141400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:38137600-38141400	Weak transcription	Right Ventricle	heart
29	chr6:38137600-38144200	Strong transcription	Spleen	Spleen
30	chr6:38138200-38142200	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:38138200-38142600	Weak transcription	Gastric	stomach
32	chr6:38138200-38143600	Weak transcription	Esophagus	oesophagus
33	chr6:38138200-38147200	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:38138400-38141400	Weak transcription	Brain Substantia Nigra	brain
35	chr6:38138400-38143800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:38138400-38144400	Weak transcription	Pancreas	Pancrea
37	chr6:38138400-38145200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:38138400-38145400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:38138400-38147200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:38138400-38147200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:38138600-38141400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr6:38138600-38145400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:38138600-38169400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:38138800-38143400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:38138800-38144200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:38138800-38144600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:38138800-38145400	Weak transcription	Fetal Brain Female	brain
48	chr6:38138800-38147200	Weak transcription	Brain Germinal Matrix	brain
49	chr6:38138800-38147200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:38139000-38141800	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links