Variant report

Variant	rs2850369
Chromosome Location	chr4:102232985-102232986
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	chr4:102229146..102231940-chr4:102232073..102233783,2	K562	blood:
2	chr4:102232326..102233842-chr4:102235389..102237956,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10007902	0.92[CEU][hapmap]
rs1031033	1.00[CEU][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1031034	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1031035	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1348161	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1441433	0.86[JPT][hapmap]
rs1530259	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549513	0.96[CEU][hapmap]
rs1549515	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs1549516	0.96[CEU][hapmap]
rs2044043	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583389	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs2583391	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2583392	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2583394	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2583395	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2583397	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2583398	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2583399	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2583402	0.81[JPT][hapmap]
rs2583406	0.87[JPT][hapmap]
rs2850326	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850328	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850329	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2850330	0.85[EUR][1000 genomes]
rs2850331	0.85[EUR][1000 genomes]
rs2850332	0.82[JPT][hapmap]
rs2850355	0.86[JPT][hapmap]
rs2850356	0.86[JPT][hapmap]
rs2850366	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850367	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850368	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850370	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850371	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850372	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850963	0.82[JPT][hapmap]
rs2850976	0.82[JPT][hapmap]
rs28664200	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4452435	0.96[CEU][hapmap]
rs920559	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2850369	AP001816.1	cis	Whole Blood	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102215400-102236600	Weak transcription	Primary B cells from cord blood	blood
2	chr4:102227800-102238200	Weak transcription	Right Ventricle	heart
3	chr4:102228200-102249400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:102228200-102250400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:102228600-102234000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:102228600-102241800	Weak transcription	HSMM	muscle
7	chr4:102228600-102247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:102228800-102235200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:102229000-102234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:102229200-102234400	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:102229400-102234400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:102229800-102236600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:102230200-102234400	Weak transcription	Psoas Muscle	Psoas
14	chr4:102230400-102234400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:102230400-102236800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:102230600-102242600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:102230800-102236800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:102230800-102241600	Weak transcription	Small Intestine	intestine
19	chr4:102231000-102238800	Weak transcription	Stomach Mucosa	stomach
20	chr4:102231400-102234200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:102231800-102234200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:102231800-102237400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr4:102232200-102241400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:102232600-102233000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:102232600-102233000	Enhancers	Spleen	Spleen
26	chr4:102232800-102233000	Enhancers	Lung	lung
27	chr4:102232800-102234400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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