Variant report

Variant	rs3949294
Chromosome Location	chr1:228115129-228115130
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11579417	0.91[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11580654	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11580665	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11581915	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11584128	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11587069	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11587085	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11589040	0.82[CEU][hapmap];0.88[TSI][hapmap]
rs11589467	0.91[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs11590118	0.81[CEU][hapmap]
rs12725747	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs13374948	0.80[CEU][hapmap]
rs28665607	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35564923	0.84[EUR][1000 genomes]
rs35826486	0.84[EUR][1000 genomes]
rs4399155	0.83[EUR][1000 genomes]
rs4653533	0.81[CEU][hapmap]
rs4653894	0.91[CEU][hapmap]
rs56910872	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57292064	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57536604	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57824519	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58398048	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6665129	0.91[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs6672422	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs6672559	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs72472998	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74140812	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs74140813	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74140814	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8192629	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[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	nsv826920	chr1:228106910-228116488	Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228098600-228117600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:228098800-228122800	Weak transcription	HSMMtube	muscle
3	chr1:228099400-228122400	Weak transcription	HSMM	muscle
4	chr1:228103800-228117000	Weak transcription	Fetal Intestine Large	intestine
5	chr1:228106600-228121400	Weak transcription	Psoas Muscle	Psoas
6	chr1:228107800-228134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:228109200-228117800	Weak transcription	Pancreas	Pancrea
8	chr1:228109600-228132000	Weak transcription	Gastric	stomach
9	chr1:228109800-228117800	Weak transcription	Lung	lung
10	chr1:228109800-228134000	Weak transcription	Right Atrium	heart
11	chr1:228111000-228129800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:228111200-228116400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:228111200-228117000	Enhancers	Fetal Muscle Trunk	muscle
14	chr1:228112000-228115200	Enhancers	Spleen	Spleen
15	chr1:228112000-228115400	Genic enhancers	Stomach Smooth Muscle	stomach
16	chr1:228112200-228115200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:228112200-228115200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:228113000-228115600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:228113000-228116200	Weak transcription	Ovary	ovary
20	chr1:228113000-228121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:228113200-228120200	Weak transcription	HMEC	breast
22	chr1:228113400-228115200	Weak transcription	Esophagus	oesophagus
23	chr1:228113400-228116200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:228113400-228118000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:228113600-228115600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:228113800-228116400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:228114000-228116200	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:228114200-228115600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:228114400-228116000	Weak transcription	Fetal Stomach	stomach
30	chr1:228114400-228121800	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:228114600-228115800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:228115000-228115400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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