Variant report

Variant	rs623454
Chromosome Location	chr10:38314891-38314892
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:38299798..38301596-chr10:38314444..38317363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189180	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10764147	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10827835	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10827836	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11011407	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1208559	0.82[ASN][1000 genomes]
rs1208592	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13503	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1735577	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200910	0.81[AMR][1000 genomes]
rs200924	0.81[AMR][1000 genomes]
rs200935	0.81[AMR][1000 genomes]
rs200936	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200937	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200939	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200943	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2144849	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2180408	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2257186	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472150	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504130	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505232	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851078	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4934916	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs496627	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs527163	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs619739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626519	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629577	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs639479	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645064	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs662945	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7069702	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7099777	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs719569	0.85[AMR][1000 genomes];0.85[EUR][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	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv550419	chr10:38311777-38501654	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs623454	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs623454	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38300400-38319600	Weak transcription	Gastric	stomach
2	chr10:38300600-38318000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:38300600-38331600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:38300600-38336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:38300600-38339400	Weak transcription	Psoas Muscle	Psoas
6	chr10:38300800-38322000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr10:38300800-38339200	Weak transcription	HSMMtube	muscle
8	chr10:38301200-38320400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr10:38301200-38325000	Weak transcription	NHLF	lung
10	chr10:38301400-38316600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:38301400-38318800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr10:38301600-38320000	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr10:38301800-38326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr10:38301800-38344400	Weak transcription	Hela-S3	cervix
15	chr10:38302400-38327400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr10:38302800-38316800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:38302800-38327200	Strong transcription	Fetal Intestine Large	intestine
18	chr10:38302800-38327400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:38303000-38316600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr10:38303200-38320200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:38303200-38326400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:38303200-38327800	Strong transcription	Primary B cells from cord blood	blood
23	chr10:38303400-38316800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:38303800-38318200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:38304200-38326400	Strong transcription	Primary T cells from cord blood	blood
26	chr10:38305000-38325600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:38305600-38319800	Strong transcription	Liver	Liver
28	chr10:38307400-38316400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr10:38307400-38321400	Weak transcription	Lung	lung
30	chr10:38307400-38321400	Weak transcription	Spleen	Spleen
31	chr10:38307400-38321600	Weak transcription	Right Ventricle	heart
32	chr10:38307600-38315600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr10:38307600-38316000	Weak transcription	Fetal Intestine Small	intestine
34	chr10:38307600-38346600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr10:38307800-38315800	Weak transcription	K562	blood
36	chr10:38307800-38321800	Weak transcription	Fetal Brain Male	brain
37	chr10:38307800-38327600	Weak transcription	NHDF-Ad	bronchial
38	chr10:38307800-38336200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr10:38307800-38336600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr10:38307800-38343600	Weak transcription	Small Intestine	intestine
41	chr10:38307800-38344000	Weak transcription	Stomach Mucosa	stomach
42	chr10:38308000-38342200	Weak transcription	Brain Angular Gyrus	brain
43	chr10:38308600-38327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:38308800-38322000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr10:38309000-38315600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr10:38309000-38315800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr10:38309000-38316400	Weak transcription	HSMM	muscle
48	chr10:38309000-38316800	Strong transcription	Fetal Brain Female	brain
49	chr10:38309000-38326400	Strong transcription	Dnd41	blood
50	chr10:38309000-38327200	Weak transcription	Fetal Heart	heart

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