Variant report

Variant	rs2250193
Chromosome Location	chr1:160951523-160951524
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160945130..160946892-chr1:160950463..160952430,2	K562	blood:
2	chr1:160939974..160941495-chr1:160951029..160953259,2	MCF-7	breast:
3	chr1:160948860..160950429-chr1:160950620..160952705,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10908820	0.80[ASN][1000 genomes]
rs12132502	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2039223	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2184065	0.84[ASN][1000 genomes]
rs2245672	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246145	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246484	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246485	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247472	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2249409	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2249933	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250304	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256505	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2256625	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265239	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2265240	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265242	0.89[AMR][1000 genomes]
rs2481073	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2481076	0.84[ASN][1000 genomes]
rs2481077	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2483139	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2483140	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2483142	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779801	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2988722	0.83[AMR][1000 genomes]
rs2990694	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2990706	0.83[EUR][1000 genomes]
rs3007155	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4483427	0.96[ASN][1000 genomes]
rs6427563	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6427571	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6677526	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6677533	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7542911	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790055	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790056	0.90[EUR][1000 genomes];0.85[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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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 miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2250193	TSTD1	cis	Adipose Subcutaneous	GTEx
rs2250193	TSTD1	cis	Nerve Tibial	GTEx
rs2250193	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160943200-160959800	Weak transcription	Pancreas	Pancrea
2	chr1:160948600-160968000	Weak transcription	Ovary	ovary
3	chr1:160951000-160951600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:160951000-160951600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr1:160951000-160951800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr1:160951000-160951800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:160951000-160951800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:160951000-160951800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:160951000-160952000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:160951000-160952000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:160951000-160952200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:160951000-160952200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:160951000-160952400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:160951200-160951600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:160951200-160951600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:160951200-160951600	Bivalent Enhancer	Adipose Nuclei	Adipose
17	chr1:160951200-160951600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:160951200-160951800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:160951200-160951800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr1:160951200-160951800	Active TSS	Psoas Muscle	Psoas
21	chr1:160951200-160952000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:160951200-160952000	Bivalent Enhancer	Fetal Brain Male	brain
23	chr1:160951200-160952200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:160951200-160952200	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr1:160951200-160952200	Active TSS	Brain Anterior Caudate	brain
26	chr1:160951200-160952200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr1:160951200-160952400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:160951200-160952400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr1:160951200-160952400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:160951200-160952400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
31	chr1:160951400-160951600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:160951400-160951600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:160951400-160951600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
34	chr1:160951400-160951600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:160951400-160951600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:160951400-160951600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
37	chr1:160951400-160951600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr1:160951400-160951600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
39	chr1:160951400-160951600	Bivalent Enhancer	Fetal Intestine Large	intestine
40	chr1:160951400-160951600	Enhancers	Placenta	Placenta
41	chr1:160951400-160951600	Bivalent Enhancer	Fetal Thymus	thymus
42	chr1:160951400-160951800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:160951400-160951800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:160951400-160951800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
45	chr1:160951400-160951800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
46	chr1:160951400-160951800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr1:160951400-160951800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
48	chr1:160951400-160951800	Bivalent Enhancer	Fetal Intestine Small	intestine
49	chr1:160951400-160951800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
50	chr1:160951400-160952000	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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