Variant report

Variant	rs10438244
Chromosome Location	chr14:104346185-104346186
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	chr14:104312778..104315212-chr14:104344720..104347233,3	MCF-7	breast:
2	chr14:104340678..104342509-chr14:104346127..104348373,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2134A5.2.1-2	chr14:104345741-104346670	XLOC_010945
2	lnc-PPP1R13B-1	chr14:104345681-104346641	NONHSAT040223
3	lnc-PPP1R13B-1	chr14:104345681-104346641	NONHSAT040224

Variant related genes	Relation type
ENSG00000258735	Chromatin interaction
ENSG00000088808	Chromatin interaction
ENSG00000258914	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10132641	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10133399	0.87[EUR][1000 genomes]
rs10135198	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10135270	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10139856	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10150898	0.82[EUR][1000 genomes]
rs10438242	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10438243	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11160769	0.87[ASN][1000 genomes]
rs11160770	0.88[ASN][1000 genomes]
rs11160771	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs11160772	0.81[JPT][hapmap]
rs12879686	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2019064	0.83[AMR][1000 genomes]
rs35551424	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35924317	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4144027	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4900601	0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55696130	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55924227	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56126771	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6576010	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66473563	0.89[ASN][1000 genomes]
rs67727470	0.88[ASN][1000 genomes]
rs71417884	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417885	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72712857	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs761985	0.80[EUR][1000 genomes]
rs8008020	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8015761	0.82[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8548	1.00[YRI][hapmap]
rs881056	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs881057	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs911338	0.82[EUR][1000 genomes]

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	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription 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 miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS 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	48 gene(s)	inside rSNPs	diseases
6	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
8	esv1838047	chr14:104283104-104359121	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS 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	20 gene(s)	inside rSNPs	diseases
9	nsv902321	chr14:104283104-104378087	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	esv1818596	chr14:104312697-104359121	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1836134	chr14:104312697-104359121	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1053305	chr14:104326137-104372608	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv542205	chr14:104326137-104372608	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv542206	chr14:104326137-104377507	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1042792	chr14:104326137-104384260	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv542207	chr14:104326137-104384260	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv1800828	chr14:104343852-104351500	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10438244	C14orf153	cis	cerebellum	SCAN
rs10438244	MARK3	cis	cerebellum	SCAN
rs10438244	TDRD9	cis	cerebellum	SCAN
rs10438244	ZFYVE21	cis	cerebellum	SCAN
rs10438244	C14orf2	cis	cerebellum	SCAN
rs10438244	TDRD9	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104339200-104346200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:104339200-104346200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:104340200-104346200	Weak transcription	Fetal Thymus	thymus
4	chr14:104341400-104346400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:104341600-104346200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr14:104341600-104346800	Weak transcription	Gastric	stomach
7	chr14:104344600-104349800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr14:104345400-104347400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr14:104345400-104347600	Flanking Active TSS	Liver	Liver
10	chr14:104345600-104346200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr14:104345600-104346200	Enhancers	Fetal Intestine Large	intestine
12	chr14:104345600-104346200	Enhancers	Fetal Intestine Small	intestine
13	chr14:104345600-104349800	Enhancers	Fetal Muscle Leg	muscle
14	chr14:104345800-104346200	Enhancers	Primary B cells from peripheral blood	blood
15	chr14:104345800-104346200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr14:104345800-104346200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
17	chr14:104345800-104346200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr14:104345800-104346200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr14:104345800-104346200	Enhancers	Adipose Nuclei	Adipose
20	chr14:104345800-104346200	Enhancers	Fetal Muscle Trunk	muscle
21	chr14:104345800-104346200	Active TSS	Rectal Smooth Muscle	rectum
22	chr14:104345800-104346200	Enhancers	Right Atrium	heart
23	chr14:104345800-104346400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr14:104345800-104346400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr14:104345800-104346400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr14:104345800-104346400	Enhancers	Ovary	ovary
27	chr14:104345800-104346400	Flanking Active TSS	Pancreas	Pancrea
28	chr14:104345800-104346800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr14:104345800-104347200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr14:104345800-104347200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr14:104345800-104347200	Flanking Active TSS	A549	lung
32	chr14:104345800-104347800	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr14:104345800-104348000	Enhancers	Fetal Kidney	kidney
34	chr14:104345800-104349600	Enhancers	Left Ventricle	heart
35	chr14:104345800-104349800	Enhancers	Esophagus	oesophagus
36	chr14:104345800-104349800	Enhancers	Right Ventricle	heart
37	chr14:104346000-104346200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr14:104346000-104346200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr14:104346000-104346200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr14:104346000-104346200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr14:104346000-104346200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr14:104346000-104346200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr14:104346000-104346200	Enhancers	Brain Cingulate Gyrus	brain
44	chr14:104346000-104346200	Enhancers	Brain Hippocampus Middle	brain
45	chr14:104346000-104346200	Enhancers	Colon Smooth Muscle	Colon
46	chr14:104346000-104346200	Flanking Active TSS	Fetal Lung	lung
47	chr14:104346000-104346200	Flanking Active TSS	Fetal Stomach	stomach
48	chr14:104346000-104346200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr14:104346000-104346200	Enhancers	Small Intestine	intestine
50	chr14:104346000-104346200	Active TSS	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links