Variant report

Variant	rs13028857
Chromosome Location	chr2:171833114-171833115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171830988..171833432-chr2:172289480..172291537,2	K562	blood:
2	chr2:171829044..171833904-chr2:172289780..172292386,7	MCF-7	breast:
3	chr2:171828467..171833455-chr2:172014696..172018339,11	K562	blood:
4	chr2:171828787..171834064-chr2:172014893..172018034,9	MCF-7	breast:
5	chr2:171785126..171787756-chr2:171828278..171833323,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction
ENSG00000115806	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10182207	0.83[EUR][1000 genomes]
rs10189480	0.82[EUR][1000 genomes]
rs10193992	0.80[EUR][1000 genomes]
rs10197081	0.82[EUR][1000 genomes]
rs10207361	0.83[EUR][1000 genomes]
rs1025242	0.83[EUR][1000 genomes]
rs1035826	0.83[EUR][1000 genomes]
rs1045327	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10515934	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803854	0.82[ASN][1000 genomes]
rs10930448	0.82[ASN][1000 genomes]
rs10930449	0.82[ASN][1000 genomes]
rs11553951	0.85[EUR][1000 genomes]
rs12151587	0.81[ASN][1000 genomes]
rs12471930	0.82[ASN][1000 genomes]
rs12612871	0.82[ASN][1000 genomes]
rs12692962	0.83[EUR][1000 genomes]
rs12996518	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12997252	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12998296	0.86[EUR][1000 genomes]
rs13000644	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13000898	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13001088	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13002517	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13003218	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13006705	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13007415	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13011011	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13026444	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13026662	0.88[ASN][1000 genomes]
rs13035460	0.80[EUR][1000 genomes]
rs13432325	0.83[EUR][1000 genomes]
rs1344236	0.82[EUR][1000 genomes]
rs1529391	0.82[ASN][1000 genomes]
rs16859066	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17281735	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1991370	0.86[EUR][1000 genomes]
rs2114738	0.88[ASN][1000 genomes]
rs2356607	0.82[EUR][1000 genomes]
rs2557799	0.88[ASN][1000 genomes]
rs28740798	0.82[EUR][1000 genomes]
rs34005022	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34017170	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34143031	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34330182	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34342928	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34532258	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34563349	0.83[EUR][1000 genomes]
rs34622740	0.83[EUR][1000 genomes]
rs34911788	0.85[EUR][1000 genomes]
rs34960296	0.82[AMR][1000 genomes]
rs35047553	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35112379	0.83[EUR][1000 genomes]
rs35123411	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35230775	0.87[ASN][1000 genomes]
rs35279794	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35332006	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35381957	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35864840	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35890547	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35987434	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755125	0.80[EUR][1000 genomes]
rs3770440	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770441	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3770442	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821090	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668355	0.82[ASN][1000 genomes]
rs55987132	0.83[EUR][1000 genomes]
rs56114146	0.86[EUR][1000 genomes]
rs6709077	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6710035	0.82[EUR][1000 genomes]
rs6714300	0.82[ASN][1000 genomes]
rs6724493	0.80[EUR][1000 genomes]
rs6742797	0.82[ASN][1000 genomes]
rs6757510	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6758331	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6761759	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6761889	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71415231	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71415232	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71415233	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72886381	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73013441	0.82[EUR][1000 genomes]
rs731692	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs731693	0.82[ASN][1000 genomes]
rs73976229	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7568083	0.82[EUR][1000 genomes]
rs7570701	0.82[ASN][1000 genomes]
rs7579424	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7585619	0.82[EUR][1000 genomes]
rs7587244	0.82[EUR][1000 genomes]
rs7593186	0.82[AMR][1000 genomes]
rs965518	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13028857	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171830400-171842200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:171830600-171902800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:171830800-171839800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:171830800-171891400	Weak transcription	Spleen	Spleen
5	chr2:171831000-171833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:171831000-171838600	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:171831000-171840000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:171831000-171847600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:171831000-171850000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:171831200-171838200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:171831200-171840400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:171831200-171843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:171831200-171845400	Weak transcription	HMEC	breast
14	chr2:171831200-171845800	Weak transcription	Osteobl	bone
15	chr2:171831200-171847000	Weak transcription	A549	lung
16	chr2:171831200-171857400	Weak transcription	HSMMtube	muscle
17	chr2:171831400-171849400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:171831400-171857000	Weak transcription	NHEK	skin
19	chr2:171831400-171879200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:171831400-171916200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:171831600-171834000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:171831600-171835800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:171831600-171840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:171832000-171844800	Weak transcription	GM12878-XiMat	blood
25	chr2:171832200-171838200	Weak transcription	K562	blood
26	chr2:171832600-171835600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:171832600-171839000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:171832600-171846000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:171832600-171852200	Weak transcription	Fetal Intestine Small	intestine
30	chr2:171833000-171848800	Weak transcription	HepG2	liver

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