Variant report

Variant	rs634106
Chromosome Location	chr1:228121548-228121549
allele	A/G
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	chr1:228083548..228086316-chr1:228121354..228124098,2	MCF-7	breast:
6	chr1:228120602..228123082-chr1:228127538..228129867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264483	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10916245	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1636192	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1774755	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2313118	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2527614	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527615	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527616	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796055	0.81[TSI][hapmap]
rs2796056	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094912	0.88[CEU][hapmap]
rs3094913	0.82[CEU][hapmap]
rs3094914	0.81[CEU][hapmap]
rs3094915	0.89[EUR][1000 genomes]
rs4653889	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs587000	0.81[TSI][hapmap]
rs590657	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs591582	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs592736	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs594916	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs596208	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596675	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605410	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs621631	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs621963	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs632832	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs635563	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs644794	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs658238	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs672907	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672977	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673726	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680148	0.81[TSI][hapmap]
rs686533	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708111	0.80[CEU][hapmap]
rs708112	0.82[CEU][hapmap]
rs708114	0.82[CEU][hapmap]
rs849903	0.94[EUR][1000 genomes]
rs849904	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs964941	0.82[CEU][hapmap];0.81[TSI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs634106	C1orf145	cis	Thyroid	GTEx
rs634106	OBSCN	cis	Esophagus Mucosa	GTEx
rs634106	WDR26	cis	cerebellum	SCAN
rs634106	GUK1	cis	parietal	SCAN

Chromatin state (count:30 , 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	chr1:228107800-228134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:228109600-228132000	Weak transcription	Gastric	stomach
5	chr1:228109800-228134000	Weak transcription	Right Atrium	heart
6	chr1:228111000-228129800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:228114400-228121800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:228116400-228122800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:228117000-228121800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:228117000-228123600	Weak transcription	Fetal Stomach	stomach
11	chr1:228118000-228125400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:228118000-228126000	Weak transcription	Esophagus	oesophagus
13	chr1:228118200-228124400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:228118400-228124600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:228118400-228133000	Weak transcription	Ovary	ovary
16	chr1:228118800-228121600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:228119000-228128000	Weak transcription	Pancreas	Pancrea
18	chr1:228120400-228122400	Weak transcription	A549	lung
19	chr1:228120600-228124800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:228121000-228121600	Genic enhancers	HMEC	breast
21	chr1:228121000-228122000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:228121000-228132600	Weak transcription	Fetal Intestine Small	intestine
23	chr1:228121200-228121600	Enhancers	Lung	lung
24	chr1:228121200-228121800	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:228121200-228123400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:228121400-228121600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:228121400-228121800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:228121400-228121800	Enhancers	Psoas Muscle	Psoas
29	chr1:228121400-228122000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:228121400-228124600	Enhancers	Skeletal Muscle Male	skeletal muscle

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