Variant report

Variant	rs7598771
Chromosome Location	chr2:234288048-234288049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1046976	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10929178	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11675254	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11675531	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11675858	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11676524	1.00[CHB][hapmap]
rs11679008	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11686188	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11694406	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs13384918	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13420688	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754595	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3796090	1.00[CHB][hapmap]
rs3796092	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs3820744	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap]
rs3828307	1.00[CHB][hapmap]
rs55684040	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55693723	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55804614	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55893802	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56082182	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56405280	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58280122	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6704644	1.00[CHB][hapmap]
rs6722763	0.86[MEX][hapmap]
rs6746234	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs6753242	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap]
rs72978363	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978374	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72978375	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72980318	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7566221	0.86[MEX][hapmap]
rs7573866	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7587876	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7598771	SP100	cis	parietal	SCAN
rs7598771	C2orf82	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234264600-234290800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:234264800-234289200	Weak transcription	Esophagus	oesophagus
4	chr2:234264800-234292800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:234265000-234295000	Weak transcription	Osteobl	bone
6	chr2:234265200-234295000	Weak transcription	NH-A	brain
7	chr2:234265800-234289400	Weak transcription	Hela-S3	cervix
8	chr2:234265800-234293000	Weak transcription	HMEC	breast
9	chr2:234266000-234292400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:234266000-234292600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:234266000-234293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:234266400-234294000	Weak transcription	Fetal Brain Male	brain
13	chr2:234268400-234293400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:234269200-234293400	Weak transcription	Right Atrium	heart
15	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:234270200-234288800	Weak transcription	Right Ventricle	heart
17	chr2:234272800-234288600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:234273000-234292200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:234274000-234295200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:234275000-234289800	Weak transcription	Pancreas	Pancrea
22	chr2:234277200-234292600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:234278600-234288600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:234278600-234291400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:234278600-234292200	Weak transcription	Ovary	ovary
27	chr2:234278600-234292800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:234278600-234292800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:234278600-234293000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:234278600-234293600	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:234278600-234293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:234278600-234294000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:234278600-234294000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:234278800-234293000	Weak transcription	Brain Substantia Nigra	brain
35	chr2:234279000-234292600	Weak transcription	NHEK	skin
36	chr2:234279000-234293000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:234279200-234288200	Weak transcription	Spleen	Spleen
38	chr2:234279200-234293200	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:234279200-234293400	Weak transcription	Brain Anterior Caudate	brain
40	chr2:234279200-234293600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:234279200-234294400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:234280400-234289200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:234280400-234294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:234280600-234293200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:234281800-234296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:234282000-234288800	Weak transcription	Left Ventricle	heart
47	chr2:234282000-234291200	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:234282000-234292000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:234282000-234292800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:234282200-234289000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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