Variant report

Variant	rs12610819
Chromosome Location	chr19:41130937-41130938
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	RCOR1	chr19:41130890-41131089	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41107019..41113650-chr19:41128672..41134191,9	K562	blood:
2	chr19:41114462..41116761-chr19:41130129..41133109,2	MCF-7	breast:
3	chr19:41108422..41113817-chr19:41128876..41134100,7	MCF-7	breast:
4	chr19:41117621..41122754-chr19:41128365..41133445,15	K562	blood:

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000266164	Chromatin interaction
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10403963	0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap]
rs10405930	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs10410606	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap]
rs1051303	0.83[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap]
rs10880	0.90[ASN][1000 genomes]
rs1131620	0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap]
rs11670451	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11671971	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864074	0.83[CHB][hapmap];0.80[GIH][hapmap]
rs1864078	0.83[CHB][hapmap]
rs2162857	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303729	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs2369006	0.83[CHB][hapmap]
rs2604902	0.83[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs28580028	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3786529	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56183542	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7254268	0.89[GIH][hapmap]
rs7257696	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap]
rs7259067	0.86[CHD][hapmap];0.80[GIH][hapmap]
rs7259237	0.83[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap]
rs7259554	0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap]
rs7367	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107014	0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised 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	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
16	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
17	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12610819	SHKBP1	Cis_1M	lymphoblastoid	RTeQTL
rs12610819	PGLYRP1	cis	cerebellum	SCAN
rs12610819	QPCTL	cis	cerebellum	SCAN
rs12610819	DMRTC2	cis	cerebellum	SCAN
rs12610819	CEACAM6	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41116600-41137000	Weak transcription	Psoas Muscle	Psoas
3	chr19:41117000-41140200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:41120400-41139800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:41120600-41133000	Weak transcription	Fetal Brain Male	brain
6	chr19:41120800-41139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:41120800-41140200	Weak transcription	Brain Anterior Caudate	brain
8	chr19:41121200-41136400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr19:41121200-41137400	Strong transcription	Fetal Muscle Leg	muscle
10	chr19:41121400-41132600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:41121400-41140200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:41121800-41136800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:41122000-41136800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:41123000-41136800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:41123200-41133400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr19:41123400-41140400	Weak transcription	Liver	Liver
17	chr19:41123800-41132600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:41124000-41133400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:41124200-41133400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr19:41124200-41136600	Weak transcription	HSMMtube	muscle
21	chr19:41124400-41133000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr19:41124400-41136000	Strong transcription	Ovary	ovary
23	chr19:41124800-41134000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr19:41124800-41136000	Strong transcription	Adipose Nuclei	Adipose
25	chr19:41124800-41136200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr19:41125000-41132800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr19:41125000-41135800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:41125200-41137200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:41125800-41136600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:41126000-41131400	Weak transcription	GM12878-XiMat	blood
31	chr19:41126000-41131600	Weak transcription	Stomach Mucosa	stomach
32	chr19:41126000-41133400	Weak transcription	Fetal Thymus	thymus
33	chr19:41126000-41139000	Weak transcription	NHDF-Ad	bronchial
34	chr19:41126000-41139800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:41126000-41140000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:41126200-41140200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:41127000-41137400	Strong transcription	Fetal Lung	lung
38	chr19:41127600-41138400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:41127600-41140200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:41128000-41133800	Strong transcription	Rectal Smooth Muscle	rectum
41	chr19:41128200-41140000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:41128800-41133600	Weak transcription	Small Intestine	intestine
43	chr19:41128800-41134800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:41128800-41140200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:41129600-41131200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:41129600-41131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:41129600-41131400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:41129600-41131400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr19:41129600-41131400	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr19:41129600-41132800	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links