Variant report

Variant	rs9425635
Chromosome Location	chr1:184663898-184663899
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	chr1:184662527..184664515-chr1:184667371..184668893,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1040666	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1046239	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1061508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1062994	0.81[AMR][1000 genomes]
rs10752941	0.85[EUR][1000 genomes]
rs10797987	0.81[EUR][1000 genomes]
rs10911633	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10911634	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10911636	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10911640	0.84[EUR][1000 genomes]
rs10911644	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs10911645	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12032144	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12043236	0.85[EUR][1000 genomes]
rs12071631	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs12124714	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12124929	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs12131285	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12184284	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12567225	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs12567226	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs2024764	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2024765	0.82[EUR][1000 genomes]
rs2024766	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2024767	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2064605	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2207733	0.85[EUR][1000 genomes]
rs2333715	1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs2333716	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs35478695	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736757	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs3895196	0.84[GIH][hapmap]
rs4469687	0.85[EUR][1000 genomes]
rs4651230	0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs6663178	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs6677073	0.86[EUR][1000 genomes]
rs726427	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7523023	0.85[EUR][1000 genomes]
rs7525074	0.85[EUR][1000 genomes]
rs861578	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs861581	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9425341	0.86[EUR][1000 genomes]
rs9425343	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9425633	0.87[EUR][1000 genomes]
rs9425634	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9658937	0.87[EUR][1000 genomes]
rs9661314	0.87[EUR][1000 genomes]
rs971080	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9787132	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS 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 target site	13 gene(s)	inside rSNPs	diseases
7	nsv1010371	chr1:184663898-184709570	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9425635	PRG4	cis	parietal	SCAN
rs9425635	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs9425635	OCLM	cis	parietal	SCAN
rs9425635	FAM129A	cis	cerebellum	SCAN
rs9425635	EDEM3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184641400-184672800	Weak transcription	Gastric	stomach
2	chr1:184653200-184705000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:184654000-184710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:184654200-184672000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:184654200-184701200	Weak transcription	Stomach Mucosa	stomach
6	chr1:184654200-184710000	Weak transcription	Esophagus	oesophagus
7	chr1:184654400-184675400	Weak transcription	Pancreas	Pancrea
8	chr1:184654600-184665800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:184654600-184672400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:184654800-184669600	Weak transcription	Fetal Lung	lung
11	chr1:184655000-184664400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:184656000-184672000	Weak transcription	HepG2	liver
13	chr1:184656400-184672800	Weak transcription	Spleen	Spleen
14	chr1:184656600-184670200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:184656600-184684000	Weak transcription	Fetal Heart	heart
16	chr1:184657000-184672600	Weak transcription	Lung	lung
17	chr1:184657200-184672800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:184657400-184672800	Weak transcription	Fetal Stomach	stomach
19	chr1:184657800-184670200	Weak transcription	HMEC	breast
20	chr1:184658400-184706800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:184658600-184665400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:184659000-184672600	Weak transcription	Aorta	Aorta
23	chr1:184659200-184668400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:184659200-184707000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:184659400-184676800	Weak transcription	Fetal Brain Male	brain
26	chr1:184660000-184704200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:184660800-184664400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:184660800-184664600	Weak transcription	NHLF	lung
29	chr1:184660800-184669200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:184660800-184680400	Weak transcription	Right Ventricle	heart
31	chr1:184661000-184665800	Strong transcription	K562	blood
32	chr1:184661000-184678600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:184661000-184705600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:184661200-184665200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:184661200-184690400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:184661200-184707800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:184661400-184666200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:184661400-184671200	Weak transcription	Fetal Kidney	kidney
39	chr1:184661400-184678600	Strong transcription	Liver	Liver
40	chr1:184661400-184690400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:184661600-184670800	Weak transcription	A549	lung
42	chr1:184661600-184672800	Weak transcription	Small Intestine	intestine
43	chr1:184661600-184693200	Strong transcription	Dnd41	blood
44	chr1:184661800-184666000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:184662000-184664400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:184662000-184665800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:184662000-184665800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:184662000-184666000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:184662000-184666000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:184662000-184666000	Strong transcription	Fetal Thymus	thymus

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