Variant report

Variant	rs7569393
Chromosome Location	chr2:210686883-210686884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:210686415..210689045-chr2:210704014..210706614,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10490022	0.85[EUR][1000 genomes]
rs10932305	0.85[CEU][hapmap]
rs10932306	0.85[EUR][1000 genomes]
rs11674672	0.88[EUR][1000 genomes]
rs11674950	0.85[EUR][1000 genomes]
rs11677476	0.88[EUR][1000 genomes]
rs11677489	0.85[EUR][1000 genomes]
rs11678044	0.92[EUR][1000 genomes]
rs11679862	0.88[EUR][1000 genomes]
rs11680007	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs11680964	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs11689771	0.85[EUR][1000 genomes]
rs11692608	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs11693202	0.85[EUR][1000 genomes]
rs11884376	0.85[EUR][1000 genomes]
rs11887161	0.85[EUR][1000 genomes]
rs11900602	0.85[EUR][1000 genomes]
rs12615516	0.85[EUR][1000 genomes]
rs12619203	0.85[EUR][1000 genomes]
rs12622305	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1476876	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1476877	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs16843453	0.81[TSI][hapmap]
rs16843614	0.81[TSI][hapmap]
rs16843618	0.81[TSI][hapmap]
rs2098204	0.92[EUR][1000 genomes]
rs2109853	1.00[ASN][1000 genomes]
rs2239672	0.81[TSI][hapmap]
rs2268042	0.81[TSI][hapmap]
rs35337581	0.88[EUR][1000 genomes]
rs35872449	0.85[EUR][1000 genomes]
rs3768813	0.81[TSI][hapmap]
rs3768814	0.81[TSI][hapmap]
rs3768826	0.81[TSI][hapmap]
rs3768835	0.81[TSI][hapmap]
rs3820746	0.85[CEU][hapmap]
rs4672559	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57305145	0.92[EUR][1000 genomes]
rs57637604	0.85[EUR][1000 genomes]
rs57990979	0.96[EUR][1000 genomes]
rs58248939	0.85[EUR][1000 genomes]
rs59373555	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60161291	0.85[EUR][1000 genomes]
rs60640585	0.85[EUR][1000 genomes]
rs61356588	0.85[EUR][1000 genomes]
rs6707679	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6716831	0.85[EUR][1000 genomes]
rs6742314	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs73074750	0.85[EUR][1000 genomes]
rs73074751	0.85[EUR][1000 genomes]
rs73074763	0.85[EUR][1000 genomes]
rs73074778	0.85[EUR][1000 genomes]
rs73074779	0.85[EUR][1000 genomes]
rs73074784	0.85[EUR][1000 genomes]
rs73074787	0.85[EUR][1000 genomes]
rs73074791	0.85[EUR][1000 genomes]
rs73074801	0.88[EUR][1000 genomes]
rs73076704	0.88[EUR][1000 genomes]
rs73076710	0.88[EUR][1000 genomes]
rs741006	0.81[TSI][hapmap]
rs7564369	0.91[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs7594601	0.81[TSI][hapmap]
rs7595017	0.85[EUR][1000 genomes]
rs975551	0.85[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs975552	0.92[CEU][hapmap];0.85[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	nsv3142	chr2:210660150-210705006	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv431969	chr2:210682494-211074494	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7569393	LANCL1	cis	lymphoblastoid	seeQTL
rs7569393	ERBB4	cis	cerebellum	SCAN
rs7569393	ATP8A1	trans	lymphoblastoid	seeQTL
rs7569393	CRIM1	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210678600-210688400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:210680000-210706800	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:210682000-210769600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:210683000-210696000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:210683600-210704000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:210683800-210704200	Weak transcription	Brain Germinal Matrix	brain
7	chr2:210685800-210687000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:210685800-210708400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:210686000-210697600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:210686000-210698400	Weak transcription	Brain Anterior Caudate	brain
11	chr2:210686000-210720400	Weak transcription	Brain Angular Gyrus	brain
12	chr2:210686200-210704000	Weak transcription	Fetal Brain Female	brain
13	chr2:210686400-210694000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:210686400-210695800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:210686400-210703800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:210686400-210705200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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