Variant report

Variant	rs583538
Chromosome Location	chr9:136638877-136638878
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136637140..136639456-chr9:136640448..136643038,2	K562	blood:
2	chr9:136637048..136639522-chr9:136645040..136647080,2	MCF-7	breast:
3	chr9:136633642..136635189-chr9:136638764..136641449,2	MCF-7	breast:
4	chr9:136636638..136643675-chr9:136644136..136648487,9	MCF-7	breast:
5	chr9:136633742..136636315-chr9:136638457..136640481,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2797825	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs2797826	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs533771	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556664	0.92[ASN][1000 genomes]
rs557430	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590614	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591797	1.00[JPT][hapmap]
rs592252	1.00[JPT][hapmap]
rs593590	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs594130	1.00[JPT][hapmap]
rs656702	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894081	chr9:136227260-136678954	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv894086	chr9:136281753-136657960	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv530972	chr9:136324358-136643044	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv870051	chr9:136459745-136656889	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv894117	chr9:136600201-136716399	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv466622	chr9:136617292-136658816	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv615691	chr9:136617292-136658816	Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv894118	chr9:136624542-136678954	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv894119	chr9:136629399-136657960	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv894120	chr9:136629399-136662638	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv894121	chr9:136629399-136692787	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv894122	chr9:136632662-136760639	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs583538	SURF6	cis	parietal	SCAN
rs583538	C9orf9	cis	parietal	SCAN
rs583538	SNORD36C	cis	parietal	SCAN
rs583538	UBAC1	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136624800-136639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:136624800-136657800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:136629400-136639000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:136631400-136639000	Weak transcription	Brain Substantia Nigra	brain
5	chr9:136632800-136641600	Strong transcription	Right Ventricle	heart
6	chr9:136633000-136639000	Weak transcription	Brain Anterior Caudate	brain
7	chr9:136633000-136639000	Weak transcription	Stomach Mucosa	stomach
8	chr9:136633000-136641000	Strong transcription	Fetal Brain Female	brain
9	chr9:136633200-136639000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:136633200-136639000	Weak transcription	NH-A	brain
11	chr9:136633200-136639200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:136633200-136647400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:136633200-136653400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:136633200-136653600	Weak transcription	Brain Angular Gyrus	brain
15	chr9:136633400-136639000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:136633400-136639800	Weak transcription	Fetal Brain Male	brain
17	chr9:136633600-136639000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:136633600-136639000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:136633600-136639000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:136633600-136639000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:136633600-136639000	Weak transcription	Thymus	Thymus
22	chr9:136633600-136640000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:136633600-136646400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr9:136633600-136646800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr9:136633800-136639000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:136633800-136639200	Strong transcription	Fetal Stomach	stomach
27	chr9:136633800-136639200	Weak transcription	Left Ventricle	heart
28	chr9:136633800-136639400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:136633800-136639400	Strong transcription	Lung	lung
30	chr9:136634000-136639000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr9:136634000-136639000	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:136634000-136639000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:136634000-136639000	Weak transcription	Ovary	ovary
34	chr9:136634000-136639000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr9:136634000-136639200	Strong transcription	Fetal Muscle Leg	muscle
36	chr9:136634000-136646400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr9:136634200-136639000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:136634200-136639000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr9:136634200-136639000	Strong transcription	Placenta	Placenta
40	chr9:136634200-136639400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:136634200-136646600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:136634600-136645000	Strong transcription	HSMMtube	muscle
43	chr9:136634600-136647400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:136634800-136639000	Strong transcription	Fetal Intestine Small	intestine
45	chr9:136634800-136639400	Strong transcription	Fetal Intestine Large	intestine
46	chr9:136635000-136639000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:136635200-136639000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:136635400-136639400	Weak transcription	Aorta	Aorta
49	chr9:136635600-136639000	Weak transcription	Colonic Mucosa	Colon
50	chr9:136635600-136639000	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links