Variant report

Variant	rs3907099
Chromosome Location	chr8:103219363-103219364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:103217322..103219597-chr8:103250656..103252706,2	K562	blood:

Variant related genes	Relation type
ENSG00000048392	Chromatin interaction
ENSG00000246263	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10505019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052069	0.85[CEU][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774420	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11774459	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11774772	1.00[GIH][hapmap]
rs11776865	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11777942	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11778107	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11783467	0.80[ASN][1000 genomes]
rs11784180	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11784534	0.94[ASN][1000 genomes]
rs11785514	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11786397	0.94[ASN][1000 genomes]
rs13261195	1.00[GIH][hapmap]
rs16869269	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs16869276	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16869282	1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs16869295	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16918482	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2293984	1.00[CHB][hapmap]
rs2305832	1.00[GIH][hapmap]
rs2387995	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28928571	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28928592	0.80[ASN][1000 genomes]
rs28928597	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28999671	0.80[ASN][1000 genomes]
rs28999676	0.80[ASN][1000 genomes]
rs28999706	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs29000274	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs29000286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs29000294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35693157	1.00[EUR][1000 genomes]
rs3735720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs3735721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735722	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4329248	0.94[ASN][1000 genomes]
rs5005121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57901015	0.94[ASN][1000 genomes]
rs57978361	0.83[ASN][1000 genomes]
rs60604862	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718165	1.00[GIH][hapmap]
rs7836046	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7841131	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer 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	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking 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	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3907099	NCALD	cis	lymphoblastoid	seeQTL
rs3907099	RRM2B	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103209600-103223000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:103209800-103219400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr8:103209800-103219600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr8:103209800-103219600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr8:103209800-103221600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:103209800-103221600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr8:103209800-103222200	Weak transcription	Left Ventricle	heart
8	chr8:103209800-103223400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr8:103209800-103223600	Weak transcription	NH-A	brain
10	chr8:103209800-103224400	Weak transcription	Fetal Intestine Large	intestine
11	chr8:103209800-103224800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr8:103209800-103225400	Weak transcription	Fetal Kidney	kidney
13	chr8:103209800-103225600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr8:103209800-103229600	Weak transcription	A549	lung
15	chr8:103209800-103229800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr8:103209800-103229800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr8:103209800-103230400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr8:103209800-103230400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:103209800-103230400	Weak transcription	Aorta	Aorta
20	chr8:103209800-103230400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr8:103209800-103230400	Weak transcription	Thymus	Thymus
22	chr8:103209800-103230800	Weak transcription	Right Ventricle	heart
23	chr8:103209800-103233400	Weak transcription	Esophagus	oesophagus
24	chr8:103209800-103233800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr8:103209800-103236800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr8:103209800-103239200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr8:103209800-103244800	Weak transcription	Stomach Mucosa	stomach
28	chr8:103210000-103219800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr8:103210000-103223000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr8:103210000-103223000	Weak transcription	Placenta	Placenta
31	chr8:103210000-103223200	Weak transcription	Fetal Thymus	thymus
32	chr8:103210000-103229800	Weak transcription	Brain Hippocampus Middle	brain
33	chr8:103210000-103230200	Weak transcription	Brain Angular Gyrus	brain
34	chr8:103210200-103219600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr8:103210200-103224400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr8:103210400-103219600	Weak transcription	NHDF-Ad	bronchial
37	chr8:103210600-103222400	Weak transcription	Fetal Muscle Leg	muscle
38	chr8:103210600-103222800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr8:103210600-103223000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr8:103210600-103225000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr8:103210600-103239600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:103210800-103232000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr8:103211000-103230400	Weak transcription	Fetal Brain Female	brain
44	chr8:103213600-103223000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr8:103214600-103222800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr8:103215000-103229600	Weak transcription	HUVEC	blood vessel
47	chr8:103215600-103248400	Weak transcription	Psoas Muscle	Psoas
48	chr8:103216000-103227400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr8:103216200-103227400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr8:103216200-103229800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links