Variant report

Variant	rs3828398
Chromosome Location	chr3:141631328-141631329
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141592835..141597303-chr3:141629979..141635181,8	MCF-7	breast:
2	chr3:141622629..141625645-chr3:141628470..141632176,3	K562	blood:
3	chr3:141629759..141632331-chr3:141657895..141659555,2	K562	blood:
4	chr3:141622390..141625561-chr3:141629742..141633540,3	K562	blood:

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10755098	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10935439	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10935440	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10935441	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10935442	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10935443	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10935446	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10935447	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11539489	0.84[ASN][1000 genomes]
rs11569259	0.80[EUR][1000 genomes]
rs11569262	0.80[EUR][1000 genomes]
rs11569278	0.80[EUR][1000 genomes]
rs11569281	0.83[EUR][1000 genomes]
rs11569291	0.83[EUR][1000 genomes]
rs11706195	0.86[ASN][1000 genomes]
rs11707100	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11707427	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11710245	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11711748	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11713023	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11721024	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs11844	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486398	0.86[ASN][1000 genomes]
rs12487977	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12487983	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490893	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12494971	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12497112	0.88[EUR][1000 genomes]
rs12497443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1560411	0.84[ASN][1000 genomes]
rs16851892	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2115935	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2288634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861382	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34071952	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36038301	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3762726	0.88[EUR][1000 genomes]
rs3792410	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3792411	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3804772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804773	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4683412	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4683413	0.80[EUR][1000 genomes]
rs4683414	0.80[EUR][1000 genomes]
rs4683638	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4683639	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4683640	0.86[ASN][1000 genomes]
rs4683641	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4683642	0.86[ASN][1000 genomes]
rs4683643	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4683644	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4683646	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4683647	0.86[ASN][1000 genomes]
rs4683649	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683651	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683652	0.95[EUR][1000 genomes]
rs55945175	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59122181	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs745966	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7616903	0.86[ASN][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3828398	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
3	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
4	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:141616200-141646600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:141618000-141633600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:141619400-141641600	Weak transcription	Ovary	ovary
9	chr3:141619600-141640200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:141619600-141644000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:141619800-141633200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:141620400-141641200	Weak transcription	Spleen	Spleen
13	chr3:141620600-141631600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:141620800-141646800	Weak transcription	Gastric	stomach
15	chr3:141621000-141646600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
17	chr3:141622000-141645000	Strong transcription	Dnd41	blood
18	chr3:141622000-141647600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:141622200-141631400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:141622200-141631600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:141622400-141631600	Strong transcription	Fetal Intestine Small	intestine
22	chr3:141622400-141647000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:141622600-141631800	Strong transcription	NHEK	skin
24	chr3:141622600-141633200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:141622600-141644800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:141623600-141652400	Strong transcription	Fetal Thymus	thymus
27	chr3:141623800-141631600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:141624200-141631800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:141624200-141632000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:141624200-141635600	Strong transcription	HMEC	breast
31	chr3:141624200-141636600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:141624400-141633400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:141624600-141649200	Weak transcription	Brain Substantia Nigra	brain
34	chr3:141625200-141632200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:141625200-141632200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:141625200-141635400	Strong transcription	NHDF-Ad	bronchial
37	chr3:141625200-141637200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr3:141625400-141635200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr3:141625600-141634200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:141625600-141647200	Weak transcription	Liver	Liver
41	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:141626000-141631800	Strong transcription	Thymus	Thymus
43	chr3:141626000-141636600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:141626200-141631800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:141626200-141631800	Strong transcription	Fetal Stomach	stomach
46	chr3:141626400-141631800	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:141626400-141642200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:141626600-141659000	Weak transcription	Pancreas	Pancrea
49	chr3:141627000-141633800	Weak transcription	Fetal Kidney	kidney
50	chr3:141627400-141646600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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