Variant report

Variant	rs10846545
Chromosome Location	chr12:124184903-124184904
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	chr12:124177268..124179844-chr12:124184486..124185994,2	K562	blood:

Variant related genes	Relation type
ENSG00000168778	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10161548	0.81[EUR][1000 genomes]
rs10773019	0.94[EUR][1000 genomes]
rs10773020	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10773021	0.84[EUR][1000 genomes]
rs10773023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773024	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773025	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10846530	0.81[EUR][1000 genomes]
rs10846532	0.94[EUR][1000 genomes]
rs10846534	0.91[EUR][1000 genomes]
rs10846536	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10846538	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10846539	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057299	0.81[EUR][1000 genomes]
rs11057304	0.81[EUR][1000 genomes]
rs11057310	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11057312	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11057313	0.91[EUR][1000 genomes]
rs11057322	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11057329	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057336	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11572940	0.91[EUR][1000 genomes]
rs11572949	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12231444	0.81[EUR][1000 genomes]
rs12308953	0.81[EUR][1000 genomes]
rs12309685	0.81[EUR][1000 genomes]
rs12313119	0.81[EUR][1000 genomes]
rs17840832	0.81[EUR][1000 genomes]
rs2292702	0.91[EUR][1000 genomes]
rs2707	0.94[EUR][1000 genomes]
rs3704	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3748271	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61154946	0.81[EUR][1000 genomes]
rs6488887	0.91[EUR][1000 genomes]
rs7302177	0.91[EUR][1000 genomes]
rs7303409	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7307219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311689	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73414223	0.81[EUR][1000 genomes]
rs7358562	0.81[EUR][1000 genomes]
rs7967780	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	esv2757517	chr12:124110122-124195856	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv2759918	chr12:124110122-124195856	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1042866	chr12:124115035-124195856	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv442292	chr12:124115047-124195854	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	esv35148	chr12:124119120-124196120	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv2756516	chr12:124119120-124196120	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv524660	chr12:124119983-124194438	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv455733	chr12:124119983-124195856	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking 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	19 gene(s)	inside rSNPs	diseases
12	nsv560496	chr12:124119983-124195856	Strong transcription Weak transcription Enhancers Active TSS Flanking 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	19 gene(s)	inside rSNPs	diseases
13	nsv560497	chr12:124129460-124195856	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv560498	chr12:124129924-124195856	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv832534	chr12:124157605-124234611	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv519344	chr12:124171903-124194438	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10846545	TCTN2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124156400-124196000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr12:124156400-124196000	Weak transcription	Thymus	Thymus
3	chr12:124156600-124189800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:124156600-124195600	Weak transcription	Esophagus	oesophagus
5	chr12:124156600-124195800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:124156600-124195800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:124156600-124196000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:124156600-124196000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:124156600-124196000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:124156600-124196000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:124156800-124186600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:124156800-124196000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:124156800-124196000	Weak transcription	HUVEC	blood vessel
14	chr12:124156800-124196200	Weak transcription	HSMM	muscle
15	chr12:124157000-124193000	Strong transcription	Fetal Stomach	stomach
16	chr12:124157000-124196000	Weak transcription	Fetal Heart	heart
17	chr12:124157000-124196000	Weak transcription	NH-A	brain
18	chr12:124158400-124193800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:124160000-124195600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:124160200-124191000	Weak transcription	Colonic Mucosa	Colon
21	chr12:124160200-124195800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:124160200-124196000	Weak transcription	Right Ventricle	heart
23	chr12:124161600-124196000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:124161800-124195800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:124164200-124186600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:124164200-124195800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:124164200-124196000	Weak transcription	Fetal Thymus	thymus
28	chr12:124166200-124195800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr12:124166800-124189000	Weak transcription	HSMMtube	muscle
30	chr12:124166800-124196000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:124168400-124187600	Strong transcription	Fetal Muscle Leg	muscle
32	chr12:124169600-124187400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:124170600-124192800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:124170800-124193200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:124172000-124185800	Weak transcription	Liver	Liver
36	chr12:124173400-124196000	Weak transcription	GM12878-XiMat	blood
37	chr12:124174200-124187600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:124174200-124187800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:124174800-124192800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:124175600-124187600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:124176000-124195800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:124176200-124187000	Weak transcription	NHEK	skin
43	chr12:124176200-124190000	Weak transcription	Spleen	Spleen
44	chr12:124176200-124195800	Weak transcription	HMEC	breast
45	chr12:124176200-124196200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:124176200-124196400	Weak transcription	Gastric	stomach
47	chr12:124177400-124189200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:124177600-124191000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:124177600-124195800	Weak transcription	Hela-S3	cervix
50	chr12:124179000-124185000	Strong transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links