Variant report

Variant	rs658238
Chromosome Location	chr1:228121291-228121292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228120545..228123784-chr1:228127076..228130229,4	K562	blood:
2	chr1:228116517..228118164-chr1:228120854..228122367,2	K562	blood:
3	chr1:228120999..228125449-chr1:228127251..228129340,4	MCF-7	breast:
4	chr1:228116517..228118419-chr1:228120867..228123021,2	K562	blood:
5	chr1:228120602..228123082-chr1:228127538..228129867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264483	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10916245	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1636192	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1774755	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2313118	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527614	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527615	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2527616	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2796056	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3094915	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653889	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590657	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591582	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs592736	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594916	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596208	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs596675	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs605410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs621372	0.81[EUR][1000 genomes]
rs621631	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs621963	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs631768	0.89[AFR][1000 genomes]
rs632832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634106	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs635563	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs644794	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs672907	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs672977	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs673726	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs686533	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs849903	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs849904	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
10	nsv873250	chr1:228051234-228121548	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
12	nsv826942	chr1:228118930-228124889	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs658238	C1orf145	cis	Thyroid	GTEx
rs658238	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228098800-228122800	Weak transcription	HSMMtube	muscle
2	chr1:228099400-228122400	Weak transcription	HSMM	muscle
3	chr1:228106600-228121400	Weak transcription	Psoas Muscle	Psoas
4	chr1:228107800-228134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:228109600-228132000	Weak transcription	Gastric	stomach
6	chr1:228109800-228134000	Weak transcription	Right Atrium	heart
7	chr1:228111000-228129800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:228113000-228121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:228114400-228121800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:228116400-228122800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:228117000-228121800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:228117000-228123600	Weak transcription	Fetal Stomach	stomach
13	chr1:228118000-228121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:228118000-228125400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:228118000-228126000	Weak transcription	Esophagus	oesophagus
16	chr1:228118200-228121400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:228118200-228121400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:228118200-228124400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:228118400-228124600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:228118400-228133000	Weak transcription	Ovary	ovary
21	chr1:228118800-228121600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:228119000-228128000	Weak transcription	Pancreas	Pancrea
23	chr1:228120400-228122400	Weak transcription	A549	lung
24	chr1:228120600-228124800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:228121000-228121600	Genic enhancers	HMEC	breast
26	chr1:228121000-228122000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:228121000-228132600	Weak transcription	Fetal Intestine Small	intestine
28	chr1:228121200-228121400	Enhancers	Spleen	Spleen
29	chr1:228121200-228121600	Enhancers	Lung	lung
30	chr1:228121200-228121800	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:228121200-228123400	Enhancers	Skeletal Muscle Female	skeletal muscle

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