Variant report

Variant	rs1339947
Chromosome Location	chr1:196431156-196431157
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:196429594..196431173-chr1:196432678..196435547,2	K562	blood:

Variant related genes	Relation type
ENSG00000162687	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10737671	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10737676	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10737678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10754192	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10754194	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10754197	0.86[EUR][1000 genomes]
rs10801536	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10922057	1.00[CHB][hapmap]
rs10922081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10922087	0.87[EUR][1000 genomes]
rs11806479	1.00[CHB][hapmap]
rs12072649	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12133987	0.87[EUR][1000 genomes]
rs12407653	1.00[JPT][hapmap]
rs1339949	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360143	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1416960	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1416966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538683	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs1556961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571489	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs16839700	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16839791	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16839832	0.82[CEU][hapmap]
rs16839841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16839848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs16839872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16839919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296269	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2335907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41451950	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4294368	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4316314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4405100	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4518841	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4562566	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4601531	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4614205	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4633231	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4658042	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4658043	0.85[EUR][1000 genomes]
rs479718	1.00[JPT][hapmap]
rs6670223	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6675592	0.92[EUR][1000 genomes]
rs6680722	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6688468	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6702610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531491	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7541165	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544202	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7544266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7552170	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][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	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196420000-196460800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:196421000-196433400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:196421800-196433400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:196422200-196432200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:196425200-196433200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:196425400-196432800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:196425400-196433800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:196425400-196434000	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:196425600-196433200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:196429000-196433600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:196429000-196435600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:196429200-196435400	Weak transcription	Ovary	ovary
13	chr1:196429200-196450400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:196430600-196431600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:196430800-196431600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:196430800-196439600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:196431000-196432000	Weak transcription	Liver	Liver

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