Variant report

Variant	rs2878749
Chromosome Location	chr1:197073932-197073933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197071674..197075370-chr1:197103633..197105995,3	K562	blood:
2	chr1:197073799..197075979-chr1:197077836..197079355,2	K562	blood:
3	chr1:196988548..196990975-chr1:197072466..197074203,2	K562	blood:
4	chr1:197055911..197057601-chr1:197071905..197074191,2	K562	blood:

Variant related genes	Relation type
ENSG00000066279	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10754216	0.89[ASN][1000 genomes]
rs10801589	0.88[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs10922163	0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1127661	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12755054	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1412635	0.82[JPT][hapmap]
rs1611982	0.86[JPT][hapmap]
rs1750311	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs17514309	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17514324	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17549312	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17549360	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17549430	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17550014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17550411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1759016	0.84[CHD][hapmap]
rs17662710	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1794011	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2225565	0.86[EUR][1000 genomes]
rs3737110	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737111	0.89[ASN][1000 genomes]
rs3748557	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs3762271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41304071	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41310925	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244139	0.81[JPT][hapmap]
rs4581302	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4628533	1.00[AFR][1000 genomes]
rs55857606	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56084994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56111948	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56387334	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5996	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61819074	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61819087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819088	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819095	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61819096	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61819116	1.00[AFR][1000 genomes]
rs61819117	1.00[AFR][1000 genomes]
rs61819118	1.00[AFR][1000 genomes]
rs61819119	0.91[AFR][1000 genomes]
rs61819124	1.00[AFR][1000 genomes]
rs61820789	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61820800	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6677930	0.81[JPT][hapmap]
rs6690730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700180	0.91[ASN][1000 genomes]
rs698859	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72736469	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72736474	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72738635	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72738637	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72738645	1.00[AFR][1000 genomes]
rs72738652	1.00[AFR][1000 genomes]
rs7410943	0.82[JPT][hapmap]
rs7514071	0.81[ASN][1000 genomes]
rs7517428	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs857024	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs857025	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs955927	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9727516	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873065	chr1:197027749-197076194	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv873068	chr1:197046782-197076194	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv873069	chr1:197055925-197109042	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2878749	F13B	cis	parietal	SCAN
rs2878749	GPR183	trans	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197052200-197074400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:197052200-197076200	Weak transcription	NHLF	lung
3	chr1:197052200-197083600	Weak transcription	Fetal Stomach	stomach
4	chr1:197052200-197106600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:197052200-197114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:197054200-197113600	Weak transcription	Fetal Kidney	kidney
7	chr1:197055000-197114200	Weak transcription	Primary B cells from cord blood	blood
8	chr1:197055600-197074000	Weak transcription	Placenta	Placenta
9	chr1:197066600-197083600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:197067000-197092200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:197070200-197076400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr1:197070400-197074000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr1:197070600-197076200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr1:197070600-197100000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:197070800-197075200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr1:197070800-197075400	ZNF genes & repeats	K562	blood
17	chr1:197070800-197078000	Strong transcription	Fetal Thymus	thymus
18	chr1:197070800-197085400	Weak transcription	Osteobl	bone
19	chr1:197071000-197074000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:197071000-197074400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
21	chr1:197071000-197084400	Weak transcription	Fetal Heart	heart
22	chr1:197071000-197105400	Strong transcription	Dnd41	blood
23	chr1:197071200-197074200	Active TSS	Brain Germinal Matrix	brain
24	chr1:197071200-197077400	Strong transcription	Fetal Lung	lung
25	chr1:197071400-197095800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:197071600-197074200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:197071600-197077800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:197071800-197074000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:197071800-197074200	Active TSS	Fetal Brain Female	brain
30	chr1:197071800-197074400	Strong transcription	HSMM	muscle
31	chr1:197071800-197104600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:197072000-197074000	Active TSS	Fetal Brain Male	brain
33	chr1:197072000-197074200	Strong transcription	NHDF-Ad	bronchial
34	chr1:197072000-197076400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:197072200-197074200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:197072400-197074000	Strong transcription	Thymus	Thymus
37	chr1:197072400-197074400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr1:197072400-197078000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:197072600-197074000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:197072600-197074000	Strong transcription	HUVEC	blood vessel
41	chr1:197072600-197078400	Strong transcription	A549	lung
42	chr1:197072600-197087400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:197072600-197104600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:197072600-197107400	Weak transcription	Fetal Intestine Small	intestine
45	chr1:197072800-197074000	Strong transcription	NH-A	brain
46	chr1:197072800-197077200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:197072800-197078600	Strong transcription	Hela-S3	cervix
48	chr1:197073000-197076600	Strong transcription	HMEC	breast
49	chr1:197073000-197078000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:197073000-197079600	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links