Variant report

Variant	rs10957370
Chromosome Location	chr8:48348333-48348334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr8:48348314-48348368	GM12878	blood:	n/a	n/a
2	RUNX3	chr8:48347997-48348376	GM12878	blood:	n/a	chr8:48348169-48348178
3	RUNX3	chr8:48348001-48348456	GM12878	blood:	n/a	chr8:48348169-48348178
4	EP300	chr8:48348043-48348414	GM12878	blood:	n/a	chr8:48348193-48348207 chr8:48348117-48348131
5	STAT1	chr8:48348205-48348354	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:48342172..48345072-chr8:48346372..48349504,3	K562	blood:
2	chr8:48345864..48348499-chr8:48349086..48353866,5	K562	blood:

Variant related genes	Relation type
SPIDR	TF binding region
ENSG00000164808	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10099236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10108778	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10109113	0.85[AFR][1000 genomes]
rs10441557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10441581	0.93[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap]
rs11776864	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12547497	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13279327	0.90[CHD][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap]
rs2130411	0.93[JPT][hapmap];0.91[YRI][hapmap]
rs2362555	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34506397	0.81[ASN][1000 genomes]
rs35332377	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4594029	0.94[ASW][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4873088	0.86[AMR][1000 genomes]
rs4873101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4873463	0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs4873478	0.93[JPT][hapmap];0.91[YRI][hapmap]
rs58299877	0.87[EUR][1000 genomes]
rs6472452	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs6473996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6981485	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6987882	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7825148	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7827571	0.94[ASW][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs7828350	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7832841	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7833589	0.88[ASW][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap]
rs7846620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1034660	chr8:48265109-48411279	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1023409	chr8:48320442-48454089	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv539595	chr8:48320442-48454089	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10957370	MCM4	cis	cerebellum	SCAN
rs10957370	MCM4	cis	lymphoblastoid	seeQTL
rs10957370	KIAA0146	cis	parietal	SCAN
rs10957370	SNAI2	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48310000-48350600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr8:48310800-48354800	Weak transcription	Right Ventricle	heart
3	chr8:48311600-48353000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr8:48312000-48349000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr8:48312200-48353000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr8:48312800-48358600	Weak transcription	Thymus	Thymus
7	chr8:48312800-48367600	Weak transcription	Pancreas	Pancrea
8	chr8:48312800-48377000	Weak transcription	Esophagus	oesophagus
9	chr8:48313200-48361000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr8:48313400-48352800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr8:48323000-48354200	Weak transcription	Spleen	Spleen
12	chr8:48323000-48364400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr8:48326000-48366000	Weak transcription	Gastric	stomach
14	chr8:48326200-48354800	Weak transcription	HMEC	breast
15	chr8:48326200-48362600	Weak transcription	Colon Smooth Muscle	Colon
16	chr8:48328400-48362600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr8:48328600-48348600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr8:48328600-48351000	Weak transcription	NHEK	skin
19	chr8:48328600-48351800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr8:48328600-48352200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr8:48328600-48352600	Weak transcription	Dnd41	blood
22	chr8:48328600-48361800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr8:48328600-48362400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:48328600-48364000	Weak transcription	Fetal Intestine Large	intestine
25	chr8:48328600-48371400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr8:48328600-48374600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr8:48328800-48350600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr8:48334600-48352800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr8:48335000-48362400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr8:48335400-48363400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr8:48335600-48352400	Weak transcription	Primary B cells from cord blood	blood
32	chr8:48337800-48357000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr8:48340200-48356800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr8:48340400-48364000	Weak transcription	Lung	lung
35	chr8:48340600-48365600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr8:48341600-48352200	Weak transcription	Brain Anterior Caudate	brain
37	chr8:48342000-48353000	Weak transcription	Right Atrium	heart
38	chr8:48342000-48362600	Weak transcription	Ovary	ovary
39	chr8:48342200-48372600	Weak transcription	Liver	Liver
40	chr8:48342600-48364000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr8:48342800-48355600	Weak transcription	Fetal Brain Female	brain
42	chr8:48343000-48354800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr8:48343800-48366800	Weak transcription	Aorta	Aorta
44	chr8:48343800-48371400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr8:48344000-48348400	Weak transcription	Primary T cells from cord blood	blood
46	chr8:48344000-48352000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr8:48344000-48352600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr8:48344200-48349200	Weak transcription	Fetal Stomach	stomach
49	chr8:48344200-48349800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr8:48344200-48350600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links