Variant report

Variant	rs10199948
Chromosome Location	chr2:39608688-39608689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
2	chr2:39592431..39595037-chr2:39606994..39609633,2	MCF-7	breast:
3	chr2:39594087..39595987-chr2:39607916..39609547,2	MCF-7	breast:
4	chr2:39608115..39611189-chr2:39665899..39668671,3	K562	blood:
5	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10196447	0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10197632	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11124671	0.89[YRI][hapmap]
rs11124672	0.80[AFR][1000 genomes]
rs11124675	0.90[YRI][hapmap]
rs11124678	0.88[AFR][1000 genomes]
rs11688033	0.84[AFR][1000 genomes]
rs11888511	0.89[EUR][1000 genomes]
rs11898025	0.89[EUR][1000 genomes]
rs12151392	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs12162306	0.87[AFR][1000 genomes]
rs12618944	0.80[AFR][1000 genomes]
rs12624242	0.84[YRI][hapmap]
rs12712642	0.83[AFR][1000 genomes]
rs17023405	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17023552	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17023573	0.89[EUR][1000 genomes]
rs17023584	0.89[EUR][1000 genomes]
rs2056655	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs2058863	0.88[AFR][1000 genomes]
rs2373530	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2373532	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs2708227	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3755171	0.85[YRI][hapmap]
rs3755176	0.90[YRI][hapmap]
rs3770661	1.00[EUR][1000 genomes]
rs3770663	0.81[YRI][hapmap]
rs4670273	0.81[JPT][hapmap]
rs4670932	0.83[ASN][1000 genomes]
rs4670938	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs55797011	1.00[EUR][1000 genomes]
rs55961227	1.00[EUR][1000 genomes]
rs56024079	0.89[EUR][1000 genomes]
rs56361338	0.89[EUR][1000 genomes]
rs56928728	1.00[EUR][1000 genomes]
rs57271382	0.89[EUR][1000 genomes]
rs59121834	0.89[EUR][1000 genomes]
rs59707152	1.00[EUR][1000 genomes]
rs61219633	1.00[EUR][1000 genomes]
rs61257289	0.89[EUR][1000 genomes]
rs6544206	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6718000	1.00[EUR][1000 genomes]
rs6720537	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs6720951	0.81[JPT][hapmap]
rs6721049	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs6731330	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6755534	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6758596	0.81[JPT][hapmap]
rs72921023	0.89[EUR][1000 genomes]
rs72927494	0.89[EUR][1000 genomes]
rs73923836	0.89[EUR][1000 genomes]
rs73923842	0.89[EUR][1000 genomes]
rs73923844	1.00[EUR][1000 genomes]
rs73923847	1.00[EUR][1000 genomes]
rs73923887	0.85[EUR][1000 genomes]
rs73923888	1.00[EUR][1000 genomes]
rs73923895	1.00[EUR][1000 genomes]
rs73924815	0.89[EUR][1000 genomes]
rs73924816	0.89[EUR][1000 genomes]
rs73924817	0.89[EUR][1000 genomes]
rs73930538	0.89[EUR][1000 genomes]
rs7581692	0.86[AFR][1000 genomes]
rs7588265	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591563	1.00[EUR][1000 genomes]
rs7595047	1.00[EUR][1000 genomes]
rs7595102	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7596222	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7597300	0.80[AFR][1000 genomes]
rs7599017	1.00[EUR][1000 genomes]
rs7605939	0.81[JPT][hapmap]
rs9309036	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs9309037	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs9309038	0.88[AFR][1000 genomes]
rs9309039	0.90[YRI][hapmap];0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
2	chr2:39588000-39608800	Weak transcription	Lung	lung
3	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
5	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:39594600-39608800	Weak transcription	Left Ventricle	heart
8	chr2:39600600-39614600	Weak transcription	Aorta	Aorta
9	chr2:39601600-39609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:39603200-39609000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
12	chr2:39603400-39612000	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:39603400-39613200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
16	chr2:39604400-39610200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:39604600-39609600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:39604600-39610400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:39604600-39610800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:39604800-39609200	Enhancers	HSMMtube	muscle
21	chr2:39605000-39608800	Weak transcription	Psoas Muscle	Psoas
22	chr2:39605000-39609000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:39605000-39609000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:39605000-39609000	Weak transcription	Right Atrium	heart
25	chr2:39605000-39609600	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:39605000-39609800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:39605200-39609000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:39605200-39609000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:39605200-39609200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:39605400-39609400	Enhancers	HSMM	muscle
31	chr2:39605600-39609600	Enhancers	Brain Hippocampus Middle	brain
32	chr2:39605600-39612400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:39605800-39612200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:39606200-39609000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:39606200-39609200	Enhancers	Liver	Liver
36	chr2:39606200-39609400	Enhancers	Brain Anterior Caudate	brain
37	chr2:39606200-39609600	Enhancers	Osteobl	bone
38	chr2:39606200-39610400	Enhancers	Fetal Heart	heart
39	chr2:39606400-39609400	Enhancers	Brain Cingulate Gyrus	brain
40	chr2:39606400-39610000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:39606400-39610000	Enhancers	Colon Smooth Muscle	Colon
42	chr2:39606400-39614000	Weak transcription	Right Ventricle	heart
43	chr2:39606600-39609200	Enhancers	NHDF-Ad	bronchial
44	chr2:39606600-39609800	Enhancers	NHLF	lung
45	chr2:39606600-39611800	Enhancers	HepG2	liver
46	chr2:39606800-39609400	Enhancers	A549	lung
47	chr2:39606800-39609800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:39606800-39610800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr2:39607000-39608800	Weak transcription	Fetal Intestine Small	intestine
50	chr2:39607000-39609600	Enhancers	Duodenum Smooth Muscle	Duodenum

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