Variant report

Variant	rs11119880
Chromosome Location	chr1:212378485-212378486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212373334..212376163-chr1:212376843..212378983,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM206-6	chr1:212378441-212378740	NONHSAT009349

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1009622	0.81[CHB][hapmap]
rs10436962	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10436976	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11119884	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs11119885	0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs11119887	0.95[EUR][1000 genomes]
rs12038888	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12041554	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12402397	0.81[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs12746096	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1389369	0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs1389370	0.82[EUR][1000 genomes]
rs1472226	0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap]
rs2012917	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs2087946	0.83[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs2307128	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2358452	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs351386	0.81[CHB][hapmap]
rs35209719	0.81[EUR][1000 genomes]
rs3816912	0.82[EUR][1000 genomes]
rs4362041	0.83[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs4500383	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951581	0.80[EUR][1000 genomes]
rs6540731	0.91[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs6540732	0.83[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs6540733	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs6540734	0.81[EUR][1000 genomes]
rs6540735	0.82[EUR][1000 genomes]
rs6657900	0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs6668866	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs6679064	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6679796	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes]
rs7511781	0.80[EUR][1000 genomes]
rs7515645	0.82[EUR][1000 genomes]
rs7519168	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7542973	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7544225	0.81[CHB][hapmap]
rs903120	0.81[EUR][1000 genomes]
rs903121	0.83[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs951623	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11119880	FCAMR	cis	parietal	SCAN
rs11119880	TMEM206	cis	Esophagus Mucosa	GTEx
rs11119880	TMEM206	cis	cerebellum	SCAN
rs11119880	SYT14	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212368800-212391000	Weak transcription	Thymus	Thymus
2	chr1:212375200-212379600	Enhancers	Placenta	Placenta
3	chr1:212376000-212382400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:212376200-212380000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:212376200-212380600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:212376400-212380600	Weak transcription	Left Ventricle	heart
7	chr1:212376800-212379000	Weak transcription	K562	blood
8	chr1:212376800-212382400	Weak transcription	HepG2	liver
9	chr1:212377600-212379800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:212378400-212379600	Weak transcription	Brain Anterior Caudate	brain

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