Variant report

Variant	rs2035400
Chromosome Location	chr3:99564441-99564442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99562459..99564499-chr3:99581056..99583363,3	MCF-7	breast:
2	chr3:99563302..99565936-chr3:99585256..99586921,2	K562	blood:
3	chr3:99562547..99565382-chr3:99565632..99567487,2	K562	blood:
4	chr3:99558033..99560301-chr3:99564115..99565654,2	MCF-7	breast:
5	chr3:99564424..99566018-chr3:99722701..99724331,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs15890	1.00[AMR][1000 genomes]
rs16841650	1.00[YRI][hapmap]
rs16841653	1.00[YRI][hapmap]
rs16841712	1.00[YRI][hapmap]
rs17313676	1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314245	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314280	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314977	1.00[EUR][1000 genomes]
rs17338576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17392822	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17393080	1.00[EUR][1000 genomes]
rs17397949	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778707	1.00[AMR][1000 genomes]
rs17778804	1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17779605	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41444055	1.00[YRI][hapmap]
rs6762809	1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772519	1.00[YRI][hapmap]
rs6784150	1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6787184	1.00[YRI][hapmap]
rs6791426	0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6794130	1.00[EUR][1000 genomes]
rs6794365	1.00[EUR][1000 genomes]
rs6803576	1.00[AMR][1000 genomes]
rs6805703	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6807615	1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808420	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7611313	1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612083	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7612089	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7619738	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625813	0.89[AFR][1000 genomes]
rs7626214	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7626310	1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628458	1.00[EUR][1000 genomes]
rs7646221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7648943	1.00[EUR][1000 genomes]
rs766777	1.00[EUR][1000 genomes]
rs768527	1.00[YRI][hapmap]
rs9756455	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99544200-99564800	Weak transcription	K562	blood
4	chr3:99551200-99566000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:99557000-99573600	Weak transcription	Small Intestine	intestine
6	chr3:99557200-99567200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:99558800-99565000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:99559000-99578000	Weak transcription	HMEC	breast
9	chr3:99561800-99565800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:99561800-99566600	Enhancers	NHDF-Ad	bronchial
11	chr3:99562000-99565000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:99562000-99565000	Enhancers	Adipose Nuclei	Adipose
13	chr3:99562000-99565600	Enhancers	HUVEC	blood vessel
14	chr3:99562200-99564800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:99562200-99573200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:99562200-99578000	Weak transcription	NHEK	skin
17	chr3:99562400-99565600	Enhancers	Left Ventricle	heart
18	chr3:99562600-99565000	Weak transcription	Brain Anterior Caudate	brain
19	chr3:99562600-99565000	Weak transcription	Fetal Heart	heart
20	chr3:99562600-99565000	Weak transcription	A549	lung
21	chr3:99562600-99565800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:99562600-99567000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:99562600-99578200	Weak transcription	Fetal Kidney	kidney
24	chr3:99562800-99565000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:99562800-99565000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr3:99562800-99566600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:99562800-99567200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:99562800-99569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:99562800-99580200	Weak transcription	Gastric	stomach
30	chr3:99563000-99565000	Weak transcription	Liver	Liver
31	chr3:99563000-99565000	Weak transcription	Right Ventricle	heart
32	chr3:99563000-99565200	Weak transcription	Fetal Intestine Small	intestine
33	chr3:99563000-99567000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:99563000-99567200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:99563000-99567200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:99563000-99567400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:99563000-99568000	Enhancers	Rectal Smooth Muscle	rectum
38	chr3:99563000-99575000	Weak transcription	Placenta	Placenta
39	chr3:99563000-99577600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:99563200-99565000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:99563200-99565000	Weak transcription	HSMMtube	muscle
42	chr3:99563200-99565400	Weak transcription	Aorta	Aorta
43	chr3:99563200-99565400	Weak transcription	NH-A	brain
44	chr3:99563200-99565600	Weak transcription	Fetal Intestine Large	intestine
45	chr3:99563200-99567200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:99563200-99567200	Weak transcription	Fetal Stomach	stomach
47	chr3:99563200-99567200	Weak transcription	Lung	lung
48	chr3:99563200-99567200	Weak transcription	Stomach Mucosa	stomach
49	chr3:99563200-99567600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:99563200-99568000	Enhancers	Colon Smooth Muscle	Colon

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