Variant report

Variant	rs2771041
Chromosome Location	chr9:108227596-108227597
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108222226..108224417-chr9:108226079..108228119,2	K562	blood:
2	chr9:108221322..108223726-chr9:108225722..108228119,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10115299	0.84[EUR][1000 genomes]
rs10761100	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10816278	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820809	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10820810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10820812	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10820813	0.91[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1327354	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1360089	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1806898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1815383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1960023	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1987634	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2225246	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2427769	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2518106	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2518112	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2518114	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2518116	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2518120	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2518123	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2518124	0.84[ASN][1000 genomes]
rs2518128	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs2518131	0.96[CEU][hapmap];0.90[YRI][hapmap];0.93[EUR][1000 genomes]
rs2768279	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2768280	0.91[EUR][1000 genomes]
rs2768283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2768290	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2768291	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2768292	0.84[ASN][1000 genomes]
rs2768294	0.96[CEU][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2771038	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2771042	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2812297	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2812303	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2812307	0.99[ASN][1000 genomes]
rs2812308	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2812310	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4742650	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4742947	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4742948	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6477447	0.83[EUR][1000 genomes]
rs6477449	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7020083	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7357632	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108212200-108234800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
4	chr9:108220200-108243400	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:108220400-108227600	Weak transcription	Liver	Liver
6	chr9:108220400-108237400	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:108220600-108227600	Weak transcription	HMEC	breast
9	chr9:108220600-108231000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:108220600-108237000	Weak transcription	Pancreas	Pancrea
11	chr9:108220600-108237400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:108220800-108229200	Weak transcription	NHLF	lung
13	chr9:108220800-108237000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:108220800-108237600	Weak transcription	Aorta	Aorta
15	chr9:108221000-108229000	Weak transcription	Lung	lung
16	chr9:108221000-108233200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:108221000-108235400	Weak transcription	Gastric	stomach
18	chr9:108221000-108236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:108221000-108237400	Weak transcription	Brain Substantia Nigra	brain
20	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
22	chr9:108221000-108266000	Weak transcription	NHEK	skin
23	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
24	chr9:108221200-108228200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:108221200-108232800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:108221200-108235000	Weak transcription	Spleen	Spleen
27	chr9:108221400-108227600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:108221400-108232200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:108221800-108236600	Weak transcription	Small Intestine	intestine
30	chr9:108221800-108238200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:108222000-108237600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:108222200-108237400	Weak transcription	Psoas Muscle	Psoas
33	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:108222200-108277000	Weak transcription	Ovary	ovary
35	chr9:108222400-108229800	Weak transcription	Fetal Intestine Small	intestine
36	chr9:108222400-108236800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr9:108222400-108242200	Weak transcription	Brain Anterior Caudate	brain
38	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
39	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
40	chr9:108223200-108252600	Weak transcription	K562	blood
41	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr9:108224800-108244000	Weak transcription	Fetal Brain Male	brain
43	chr9:108225000-108237000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr9:108225000-108249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:108225800-108233600	Strong transcription	A549	lung
46	chr9:108226200-108228200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:108226400-108228200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:108226400-108228200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:108226400-108232200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:108226400-108232400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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