Variant report

Variant	rs6698889
Chromosome Location	chr1:161699906-161699907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161591405..161593904-chr1:161697560..161699954,2	K562	blood:
2	chr1:161697451..161700405-chr1:161734526..161737492,2	K562	blood:
3	chr1:161645664..161648632-chr1:161696817..161700044,3	K562	blood:

Variant related genes	Relation type
ENSG00000226889	Chromatin interaction
ENSG00000118217	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11810305	0.87[ASN][1000 genomes]
rs1503812	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1503813	0.89[ASN][1000 genomes]
rs2840310	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs905589	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][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
rs6698889	FCRLA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161697600-161700200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:161697600-161700200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:161697600-161700200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr1:161697600-161700800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:161697600-161700800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr1:161697600-161700800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:161697800-161700000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:161697800-161700000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:161697800-161700000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:161697800-161700000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:161697800-161700600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:161697800-161700600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:161697800-161700800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:161697800-161700800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:161697800-161700800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:161697800-161700800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:161697800-161706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:161698000-161700000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:161698000-161700000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:161698000-161700000	Weak transcription	NH-A	brain
21	chr1:161698000-161700000	Weak transcription	NHLF	lung
22	chr1:161698000-161700000	Weak transcription	Osteobl	bone
23	chr1:161698000-161700400	Weak transcription	Primary B cells from cord blood	blood
24	chr1:161698000-161700600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:161698000-161702600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:161698000-161703400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:161698000-161703400	Enhancers	K562	blood
28	chr1:161698000-161706000	Enhancers	NHEK	skin
29	chr1:161698000-161707600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:161698200-161700400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:161698400-161700400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
32	chr1:161698400-161700600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:161698400-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:161698600-161700200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:161698600-161700800	Enhancers	NHDF-Ad	bronchial
36	chr1:161698600-161705600	Weak transcription	A549	lung
37	chr1:161698800-161702600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:161699200-161700000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:161699200-161700000	Enhancers	GM12878-XiMat	blood
40	chr1:161699200-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:161699200-161707400	Enhancers	HMEC	breast
42	chr1:161699400-161700800	Enhancers	HUVEC	blood vessel
43	chr1:161699600-161700600	Enhancers	HSMM	muscle
44	chr1:161699600-161700800	Enhancers	Hela-S3	cervix
45	chr1:161699800-161700800	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links