Variant report

Variant	rs2000104
Chromosome Location	chr1:161698194-161698195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161591405..161593904-chr1:161697560..161699954,2	K562	blood:
2	chr1:161696233..161698594-chr1:161718488..161721013,2	MCF-7	breast:
3	chr1:161696482..161699035-chr1:161718061..161722028,6	K562	blood:
4	chr1:161657417..161659539-chr1:161696325..161698709,3	K562	blood:
5	chr1:161648385..161650314-chr1:161696093..161698220,2	K562	blood:
6	chr1:161696672..161698764-chr1:161719597..161721628,3	K562	blood:
7	chr1:161654373..161658306-chr1:161696464..161699587,3	MCF-7	breast:
8	chr1:161694367..161698874-chr1:161718174..161721030,6	MCF-7	breast:
9	chr1:161651291..161653505-chr1:161696476..161699114,3	K562	blood:
10	chr1:161697451..161700405-chr1:161734526..161737492,2	K562	blood:
11	chr1:161695918..161698329-chr1:161735226..161737077,2	MCF-7	breast:
12	chr1:161535342..161537175-chr1:161695826..161698506,2	MCF-7	breast:
13	chr1:161696821..161698460-chr1:161718041..161719561,2	K562	blood:
14	chr1:161640986..161643411-chr1:161696404..161699095,2	MCF-7	breast:
15	chr1:161645664..161648632-chr1:161696817..161700044,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226889	Chromatin interaction
ENSG00000081721	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000213075	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1503809	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7520519	0.93[EUR][1000 genomes]
rs905591	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
5	nsv516773	chr1:161691433-161702763	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
6	nsv464195	chr1:161693003-161702792	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
7	nsv548076	chr1:161693003-161702792	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2000104	FCRLA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161695400-161698200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:161696200-161698200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:161696400-161698200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:161697600-161698200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
5	chr1:161697600-161698400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:161697600-161698400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:161697600-161698400	Weak transcription	Right Ventricle	heart
8	chr1:161697600-161698600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:161697600-161699600	Weak transcription	Hela-S3	cervix
10	chr1:161697600-161700200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:161697600-161700200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:161697600-161700200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:161697600-161700800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:161697600-161700800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:161697600-161700800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:161697800-161698200	Enhancers	Fetal Brain Male	brain
17	chr1:161697800-161698400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:161697800-161698400	Enhancers	Liver	Liver
19	chr1:161697800-161698600	Enhancers	Primary T cells from cord blood	blood
20	chr1:161697800-161698600	Enhancers	Dnd41	blood
21	chr1:161697800-161698800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:161697800-161698800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:161697800-161699200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:161697800-161699400	Weak transcription	HUVEC	blood vessel
25	chr1:161697800-161700000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:161697800-161700000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:161697800-161700000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:161697800-161700000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:161697800-161700600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:161697800-161700600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:161697800-161700800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr1:161697800-161700800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:161697800-161700800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:161697800-161700800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:161697800-161706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:161698000-161698200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:161698000-161698400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:161698000-161698400	Weak transcription	A549	lung
39	chr1:161698000-161698400	Enhancers	GM12878-XiMat	blood
40	chr1:161698000-161698600	Weak transcription	NHDF-Ad	bronchial
41	chr1:161698000-161699200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:161698000-161699200	Weak transcription	HMEC	breast
43	chr1:161698000-161699600	Weak transcription	HSMM	muscle
44	chr1:161698000-161699800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:161698000-161700000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:161698000-161700000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:161698000-161700000	Weak transcription	NH-A	brain
48	chr1:161698000-161700000	Weak transcription	NHLF	lung
49	chr1:161698000-161700000	Weak transcription	Osteobl	bone
50	chr1:161698000-161700400	Weak transcription	Primary B cells from cord blood	blood

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