Variant report

Variant	rs1341988
Chromosome Location	chr1:223429237-223429238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223428944..223431971-chr1:223436003..223438459,3	K562	blood:
2	chr1:223314112..223315763-chr1:223428668..223430244,2	MCF-7	breast:
3	chr1:223427403..223430031-chr1:223430338..223431900,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10495206	0.82[JPT][hapmap]
rs1400959	0.82[JPT][hapmap]
rs1400963	0.82[JPT][hapmap]
rs1418150	0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1640849	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17479856	0.83[GIH][hapmap];0.91[JPT][hapmap]
rs17480087	0.82[JPT][hapmap]
rs17518349	0.82[JPT][hapmap]
rs17518363	0.82[JPT][hapmap]
rs17538964	0.80[GIH][hapmap];0.91[JPT][hapmap]
rs17539269	0.82[JPT][hapmap]
rs61837626	0.83[ASN][1000 genomes]
rs61837627	0.83[ASN][1000 genomes]
rs851202	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs851203	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs851216	0.81[CEU][hapmap]

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	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1341988	SUSD4	cis	parietal	SCAN
rs1341988	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223423800-223439600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:223424200-223438800	Weak transcription	Ovary	ovary
3	chr1:223424400-223431800	Weak transcription	Fetal Intestine Small	intestine
4	chr1:223427400-223442000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:223428200-223429600	Weak transcription	Primary T cells from cord blood	blood
6	chr1:223428400-223432200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:223428800-223430200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:223429000-223429600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:223429000-223429600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:223429000-223429800	Enhancers	Stomach Mucosa	stomach
11	chr1:223429000-223430200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:223429000-223430200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:223429000-223430200	Enhancers	Esophagus	oesophagus
14	chr1:223429000-223430200	Enhancers	NHEK	skin
15	chr1:223429000-223430400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:223429000-223430400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:223429200-223429400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
18	chr1:223429200-223429600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr1:223429200-223429600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr1:223429200-223429800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:223429200-223429800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr1:223429200-223429800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:223429200-223429800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:223429200-223429800	Enhancers	A549	lung
25	chr1:223429200-223430400	Enhancers	HMEC	breast

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