Variant report

Variant	rs2029356
Chromosome Location	chr1:92209311-92209312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92197202..92203288-chr1:92206365..92210533,5	K562	blood:
2	chr1:92206771..92209600-chr1:92218197..92220922,3	K562	blood:
3	chr1:92208195..92211012-chr1:92213162..92216237,4	K562	blood:
4	chr1:92207711..92209549-chr1:92218107..92220194,2	K562	blood:
5	chr1:92207551..92212491-chr1:92212891..92216237,4	K562	blood:
6	chr1:92196725..92200248-chr1:92206849..92210560,4	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11165377	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165390	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs11165399	0.99[ASN][1000 genomes]
rs11165410	0.98[ASN][1000 genomes]
rs11801868	0.99[ASN][1000 genomes]
rs12061269	0.99[ASN][1000 genomes]
rs12066159	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs12067583	0.99[ASN][1000 genomes]
rs12076549	0.95[CHB][hapmap];0.85[CHD][hapmap]
rs12123737	0.80[ASN][1000 genomes]
rs17513917	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs284876	0.84[CHB][hapmap]
rs4658112	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2029356	BTBD8	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92197000-92215200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:92197200-92215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:92197600-92230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:92197800-92211000	Weak transcription	Colonic Mucosa	Colon
5	chr1:92198000-92210400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:92198200-92224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:92198400-92210400	Weak transcription	HUVEC	blood vessel
8	chr1:92199200-92218600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:92199400-92219000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:92201200-92219000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:92201400-92217600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:92203000-92210400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:92203200-92210200	Weak transcription	Brain Anterior Caudate	brain
14	chr1:92203200-92210400	Weak transcription	Stomach Mucosa	stomach
15	chr1:92203200-92212800	Weak transcription	Spleen	Spleen
16	chr1:92203400-92209400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:92203400-92210200	Weak transcription	Fetal Intestine Large	intestine
18	chr1:92204800-92247000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:92205000-92212400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:92206200-92212000	Enhancers	Colon Smooth Muscle	Colon
21	chr1:92206200-92212400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:92206200-92213600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:92206400-92209600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:92206400-92209800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:92206600-92209400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:92206600-92209400	Enhancers	Left Ventricle	heart
27	chr1:92206800-92209400	Strong transcription	Placenta	Placenta
28	chr1:92206800-92209400	Enhancers	Pancreas	Pancrea
29	chr1:92207000-92209600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:92207000-92209800	Enhancers	Ovary	ovary
31	chr1:92207200-92209400	Enhancers	Right Atrium	heart
32	chr1:92207200-92210400	Weak transcription	K562	blood
33	chr1:92207400-92209400	Enhancers	Esophagus	oesophagus
34	chr1:92207400-92210600	Genic enhancers	NHDF-Ad	bronchial
35	chr1:92207600-92209400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:92207600-92209400	Genic enhancers	Fetal Muscle Leg	muscle
37	chr1:92207600-92209400	Enhancers	Psoas Muscle	Psoas
38	chr1:92207600-92211400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:92207800-92209600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr1:92207800-92211200	Weak transcription	A549	lung
41	chr1:92208000-92209600	Enhancers	Adipose Nuclei	Adipose
42	chr1:92208000-92210600	Weak transcription	Aorta	Aorta
43	chr1:92208200-92209400	Enhancers	Rectal Smooth Muscle	rectum
44	chr1:92208200-92209400	Enhancers	Hela-S3	cervix
45	chr1:92208200-92209400	Genic enhancers	HepG2	liver
46	chr1:92208200-92210000	Weak transcription	Fetal Kidney	kidney
47	chr1:92208400-92209400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:92208400-92235800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:92208800-92209400	Enhancers	Stomach Smooth Muscle	stomach
50	chr1:92208800-92209600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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