Variant report

Variant	rs10744161
Chromosome Location	chr12:124231355-124231356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124230572..124233119-chr12:124233359..124235120,2	K562	blood:

Variant related genes	Relation type
ENSG00000185344	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10160842	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10160937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1040156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1051793	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1060637	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734903	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734904	0.90[EUR][1000 genomes]
rs10734905	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734906	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734908	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10744157	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744159	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10744162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10773026	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773030	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773031	0.82[EUR][1000 genomes]
rs10773032	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10773033	0.94[EUR][1000 genomes]
rs10773034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10846537	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10846549	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846550	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10846551	0.82[EUR][1000 genomes]
rs10846553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1139789	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11572920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11572952	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11609591	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611354	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612030	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612479	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612927	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs11613632	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11837144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12580486	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12817757	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12820195	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12821242	0.84[CEU][hapmap]
rs12827074	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12829893	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12830927	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1399961	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1515815	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1878077	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2176152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2222060	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2271660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271661	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271662	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2333835	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2333836	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333837	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2333838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333839	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34247974	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4930708	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488888	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6488893	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488897	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488899	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6488900	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6488902	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7132115	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7133199	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134074	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7135542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7135660	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136939	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7137946	0.81[CEU][hapmap]
rs7139193	0.81[CEU][hapmap]
rs7294984	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7295552	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7297576	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298440	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298831	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7300721	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7300818	0.86[EUR][1000 genomes]
rs7301641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7302649	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7302708	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7306549	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7307008	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7307343	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7308234	0.83[CEU][hapmap]
rs7308398	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308862	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7309528	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7310918	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7311789	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7313032	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7313261	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7397240	0.82[EUR][1000 genomes]
rs7397745	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7397746	0.91[EUR][1000 genomes]
rs7398082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7398384	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7398606	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7398641	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7398851	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7399128	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7399224	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7953599	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7956045	0.84[EUR][1000 genomes]
rs7956751	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7958693	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7959553	0.85[CEU][hapmap]
rs7960403	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7963968	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7964443	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7966867	0.81[CEU][hapmap]
rs7973155	0.84[CEU][hapmap]
rs7973695	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7974279	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7974331	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974462	0.85[EUR][1000 genomes]
rs7975119	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7975233	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7978447	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7979528	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs882563	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs968203	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9787987	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788204	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10744161	TCTN2	cis	Artery Tibial	GTEx
rs10744161	TCTN2	cis	Adipose Subcutaneous	GTEx
rs10744161	TCTN2	cis	Esophagus Muscularis	GTEx
rs10744161	TCTN2	cis	Stomach	GTEx
rs10744161	TCTN2	cis	Nerve Tibial	GTEx
rs10744161	TCTN2	cis	lung	GTEx
rs10744161	DDX55	cis	Brain Pons	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124197600-124234400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:124201800-124247800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:124202200-124242600	Strong transcription	Fetal Stomach	stomach
4	chr12:124202600-124245200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:124202600-124245200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:124203400-124239800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:124203600-124242400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:124203600-124242400	Strong transcription	Fetal Muscle Leg	muscle
9	chr12:124203600-124244600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:124203600-124246000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:124203800-124240000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:124203800-124245000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:124203800-124248000	Strong transcription	Dnd41	blood
14	chr12:124204000-124235200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:124204000-124235800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr12:124204000-124239800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:124205000-124242400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:124205400-124233200	Weak transcription	Stomach Mucosa	stomach
19	chr12:124206000-124241800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:124206200-124237200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:124206400-124237600	Strong transcription	Adipose Nuclei	Adipose
22	chr12:124208800-124244800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:124209200-124236000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr12:124209200-124242600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:124209800-124239600	Strong transcription	Brain Germinal Matrix	brain
26	chr12:124213000-124243400	Strong transcription	Fetal Intestine Small	intestine
27	chr12:124215400-124236200	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr12:124215400-124242600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:124215400-124244800	Strong transcription	Liver	Liver
30	chr12:124215800-124240000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr12:124215800-124242400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr12:124216000-124232200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:124217200-124240000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:124217400-124239800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:124220200-124236200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:124221800-124246200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:124222000-124233000	Weak transcription	Fetal Brain Male	brain
38	chr12:124223200-124240000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:124223400-124240000	Strong transcription	Fetal Intestine Large	intestine
40	chr12:124223800-124232000	Weak transcription	Fetal Heart	heart
41	chr12:124224200-124233400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:124224200-124238800	Weak transcription	Fetal Kidney	kidney
43	chr12:124224200-124246400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:124225600-124232200	Strong transcription	Brain Cingulate Gyrus	brain
45	chr12:124226200-124239600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:124226800-124233600	Weak transcription	Small Intestine	intestine
47	chr12:124227000-124233600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr12:124227000-124233600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:124227800-124232400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:124228000-124236000	Strong transcription	Primary T cells fromperipheralblood	blood

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