Variant report

Variant	rs1229665
Chromosome Location	chr7:26440133-26440134
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	chr7:26438613..26440865-chr7:26441029..26444147,3	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1013687	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1229653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1229655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1229661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1229668	1.00[ASN][1000 genomes]
rs1234952	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1229665	CHN2	cis	parietal	SCAN
rs1229665	LOC441204	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26438600-26440200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:26438600-26440200	Flanking Active TSS	Fetal Brain Male	brain
3	chr7:26439000-26452200	Weak transcription	Ovary	ovary
4	chr7:26439000-26452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:26439000-26453000	Weak transcription	Lung	lung
6	chr7:26439200-26440200	Enhancers	Primary B cells from cord blood	blood
7	chr7:26439200-26440400	Enhancers	Primary B cells from peripheral blood	blood
8	chr7:26439200-26444000	Weak transcription	Liver	Liver
9	chr7:26439200-26444200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:26439400-26440200	Flanking Active TSS	Fetal Kidney	kidney
11	chr7:26439600-26440800	Enhancers	Primary hematopoietic stem cells	blood
12	chr7:26439600-26443800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:26439600-26443800	Weak transcription	A549	lung
14	chr7:26439800-26440400	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr7:26439800-26440800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:26439800-26443400	Weak transcription	Fetal Lung	lung
17	chr7:26439800-26443600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:26439800-26443800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:26439800-26453000	Weak transcription	Pancreas	Pancrea
20	chr7:26440000-26440800	Enhancers	Brain Germinal Matrix	brain
21	chr7:26440000-26441000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr7:26440000-26441400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:26440000-26443200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr7:26440000-26443200	Weak transcription	K562	blood
25	chr7:26440000-26444200	Weak transcription	Fetal Brain Female	brain
26	chr7:26440000-26444400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:26440000-26444600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:26440000-26445200	Weak transcription	Fetal Stomach	stomach

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