Variant report

Variant	rs35209719
Chromosome Location	chr1:212401677-212401678
allele	A/C
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	FOXA2	chr1:212401496-212402652	HepG2	liver:	n/a	n/a
2	REST	chr1:212401539-212401742	SK-N-SH	brain:	n/a	chr1:212401689-212401698 chr1:212401638-212401656
3	GATA3	chr1:212401292-212401858	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000226251	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10863953	0.86[EUR][1000 genomes]
rs10863954	0.86[EUR][1000 genomes]
rs11119879	0.86[EUR][1000 genomes]
rs11119880	0.81[EUR][1000 genomes]
rs11119883	0.88[EUR][1000 genomes]
rs11119884	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119885	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119887	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12028026	0.89[EUR][1000 genomes]
rs12038888	0.81[EUR][1000 genomes]
rs12073206	0.89[EUR][1000 genomes]
rs12402397	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389369	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389370	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472226	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967114	0.87[EUR][1000 genomes]
rs1967116	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1967117	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001234	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012917	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2087946	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307128	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884512	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816912	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4362041	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4500383	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4558048	0.86[EUR][1000 genomes]
rs4951581	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951582	0.84[ASN][1000 genomes]
rs6540729	0.88[EUR][1000 genomes]
rs6540731	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540732	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540733	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540734	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540735	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657900	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6668866	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6679796	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695681	0.89[EUR][1000 genomes]
rs7511781	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515645	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518329	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519168	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530375	0.86[EUR][1000 genomes]
rs7537062	0.89[EUR][1000 genomes]
rs7542973	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7544225	0.82[ASN][1000 genomes]
rs7552021	0.88[EUR][1000 genomes]
rs867584	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903120	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903121	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951623	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35209719	TMEM206	cis	Esophagus Mucosa	GTEx
rs35209719	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212392600-212404800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:212398000-212402000	Enhancers	HepG2	liver
3	chr1:212398600-212402000	Enhancers	Liver	Liver
4	chr1:212398800-212402600	Enhancers	Stomach Mucosa	stomach
5	chr1:212399000-212403200	Enhancers	Fetal Heart	heart
6	chr1:212399400-212401800	Weak transcription	Fetal Lung	lung
7	chr1:212399400-212405200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:212399600-212403200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:212399600-212404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:212399600-212404800	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:212399800-212403200	Weak transcription	Right Ventricle	heart
12	chr1:212399800-212403800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:212399800-212405200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:212399800-212406600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:212399800-212407800	Weak transcription	Brain Anterior Caudate	brain
16	chr1:212400000-212404800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:212400000-212405000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:212400000-212405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:212400000-212405200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:212400000-212405200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:212400000-212405200	Weak transcription	Fetal Thymus	thymus
22	chr1:212400000-212407600	Weak transcription	Spleen	Spleen
23	chr1:212400000-212407800	Weak transcription	Right Atrium	heart
24	chr1:212400000-212407800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:212400200-212405400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:212400200-212406800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:212400600-212404200	Enhancers	Pancreas	Pancrea
28	chr1:212400800-212402800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:212401000-212401800	Enhancers	Gastric	stomach
30	chr1:212401000-212402400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:212401000-212402600	Enhancers	NHDF-Ad	bronchial
32	chr1:212401200-212403000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:212401200-212404200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:212401400-212403200	Weak transcription	Small Intestine	intestine
35	chr1:212401400-212408400	Weak transcription	Lung	lung
36	chr1:212401600-212401800	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr1:212401600-212401800	Enhancers	Left Ventricle	heart
38	chr1:212401600-212402000	Enhancers	A549	lung
39	chr1:212401600-212402600	Enhancers	Fetal Kidney	kidney
40	chr1:212401600-212402800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:212401600-212403400	Enhancers	Fetal Intestine Large	intestine
42	chr1:212401600-212403400	Enhancers	Fetal Intestine Small	intestine
43	chr1:212401600-212405000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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