Variant report

Variant	rs1441433
Chromosome Location	chr4:102209360-102209361
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102208778..102209725-chr4:102317892..102318526,2	MCF-7	breast:
2	chr4:102199385..102202283-chr4:102207975..102210015,2	MCF-7	breast:
3	chr4:102206153..102209881-chr4:102222002..102225867,4	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10007902	0.81[JPT][hapmap]
rs1031033	0.95[JPT][hapmap]
rs1031034	0.95[JPT][hapmap]
rs1348161	0.95[JPT][hapmap]
rs1530259	0.95[JPT][hapmap]
rs1549513	0.81[JPT][hapmap]
rs1549515	0.83[JPT][hapmap]
rs1549516	0.81[JPT][hapmap]
rs1561719	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2028475	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2099813	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2583389	0.95[JPT][hapmap]
rs2583392	0.95[JPT][hapmap]
rs2583394	0.95[JPT][hapmap]
rs2583395	0.95[JPT][hapmap]
rs2583398	0.95[JPT][hapmap]
rs2583399	0.95[JPT][hapmap]
rs2583400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2583401	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2583402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2583406	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2583410	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850326	0.95[JPT][hapmap]
rs2850332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2850339	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850344	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850348	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850349	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850350	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850352	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850354	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850355	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850356	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850357	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850358	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2850360	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850367	0.95[JPT][hapmap]
rs2850369	0.86[JPT][hapmap]
rs2850370	0.95[JPT][hapmap]
rs2850371	0.95[JPT][hapmap]
rs2850954	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850967	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850969	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850974	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850975	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2850976	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4452435	0.81[JPT][hapmap]
rs755961	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs920559	0.93[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes]
rs920560	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs962384	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1441433	FLJ20021	cis	multi-tissue	Pritchard
rs1441433	FRAT1	trans	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102199600-102210400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr4:102200000-102211800	Weak transcription	HMEC	breast
3	chr4:102200600-102211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:102201000-102213000	Weak transcription	Fetal Heart	heart
5	chr4:102201200-102218200	Weak transcription	NHEK	skin
6	chr4:102201400-102214200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:102202200-102210600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:102203800-102209400	Weak transcription	Brain Angular Gyrus	brain
9	chr4:102204000-102209600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:102204400-102209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:102204800-102211200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:102205000-102212600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:102205200-102210600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:102206200-102210200	Enhancers	Ovary	ovary
15	chr4:102206200-102210200	Enhancers	Psoas Muscle	Psoas
16	chr4:102206400-102209400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:102206600-102210600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:102206800-102210400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr4:102207000-102216600	Weak transcription	NH-A	brain
20	chr4:102207200-102210000	Weak transcription	HUVEC	blood vessel
21	chr4:102207200-102212000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:102207400-102209800	Weak transcription	NHDF-Ad	bronchial
23	chr4:102207400-102209800	Weak transcription	Osteobl	bone
24	chr4:102207400-102212000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:102207400-102212000	Weak transcription	Gastric	stomach
26	chr4:102207400-102214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:102207400-102214200	Weak transcription	Esophagus	oesophagus
28	chr4:102207600-102209600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:102207600-102211400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:102207600-102226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:102207800-102209400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr4:102207800-102210200	Enhancers	Adipose Nuclei	Adipose
33	chr4:102208000-102211200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:102208000-102212400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:102208200-102210600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:102208200-102210600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr4:102208400-102210200	Enhancers	Colon Smooth Muscle	Colon
38	chr4:102208400-102210800	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr4:102208400-102211200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:102208600-102209400	Enhancers	H9 Cell Line	embryonic stem cell
41	chr4:102208600-102209400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:102208600-102209400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:102208600-102209400	Enhancers	Rectal Smooth Muscle	rectum
44	chr4:102208600-102209400	Enhancers	Right Ventricle	heart
45	chr4:102208600-102209600	Enhancers	Pancreas	Pancrea
46	chr4:102208600-102209800	Enhancers	Primary hematopoietic stem cells	blood
47	chr4:102208600-102209800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr4:102208600-102209800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:102208600-102209800	Enhancers	Brain Hippocampus Middle	brain
50	chr4:102208600-102209800	Enhancers	A549	lung

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