Variant report

Variant	rs607941
Chromosome Location	chr1:10539543-10539544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10536268..10539627-chr1:10553457..10556201,3	K562	blood:
2	chr1:10536910..10540005-chr1:10543843..10547119,3	K562	blood:
3	chr1:10534889..10536510-chr1:10537915..10540242,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10864458	0.87[EUR][1000 genomes]
rs10864459	0.95[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs10864460	0.95[CEU][hapmap]
rs11121587	0.82[CHB][hapmap]
rs1152739	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1188525	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1188526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1188528	0.91[EUR][1000 genomes]
rs1188529	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12028449	0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs12375	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1307489	0.92[CHB][hapmap]
rs1307490	0.84[CHB][hapmap]
rs1307494	0.84[CHB][hapmap]
rs1307497	0.84[CHB][hapmap]
rs1308520	0.92[CHB][hapmap]
rs1411402	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1632108	0.98[EUR][1000 genomes]
rs17035305	0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2026792	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2056417	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2480777	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2480782	0.82[CHB][hapmap]
rs2480784	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2480785	0.87[EUR][1000 genomes]
rs2483677	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2483686	0.92[CHB][hapmap]
rs2506880	0.85[EUR][1000 genomes]
rs2506892	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2506901	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2506902	1.00[CEU][hapmap]
rs2781230	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs2781232	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2847337	0.92[CHB][hapmap]
rs2847344	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs544289	0.84[CHB][hapmap]
rs585870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs587916	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs589400	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs596537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597438	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616402	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs616488	0.91[GIH][hapmap];0.82[TSI][hapmap]
rs617728	0.88[EUR][1000 genomes]
rs620405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs622623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636291	0.95[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs648324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs648399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs652771	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540931	0.90[CHB][hapmap]
rs6540933	1.00[EUR][1000 genomes]
rs657244	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs660725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6687430	0.84[CHD][hapmap]
rs668805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs669701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs683864	0.98[EUR][1000 genomes]
rs684016	0.81[AFR][1000 genomes]
rs685746	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs944973	0.84[CHB][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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs607941	AADACL3	cis	parietal	SCAN
rs607941	PLEKHG5	cis	parietal	SCAN
rs607941	SLC2A5	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10535800-10555000	Weak transcription	Aorta	Aorta
2	chr1:10536000-10544800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:10536000-10548200	Weak transcription	Ovary	ovary
4	chr1:10536000-10549800	Weak transcription	Gastric	stomach
5	chr1:10536000-10549800	Weak transcription	Left Ventricle	heart
6	chr1:10536000-10550200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:10536000-10555000	Weak transcription	Esophagus	oesophagus
8	chr1:10536000-10555000	Weak transcription	HSMMtube	muscle
9	chr1:10536000-10555600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:10536200-10544400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:10536200-10544800	Weak transcription	Osteobl	bone
12	chr1:10536200-10555000	Weak transcription	NH-A	brain
13	chr1:10536400-10541400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:10536400-10541600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:10536400-10544200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:10536400-10549400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:10536400-10549400	Weak transcription	A549	lung
18	chr1:10536400-10549600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:10536400-10549800	Weak transcription	Primary B cells from cord blood	blood
20	chr1:10536400-10550000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:10536400-10550000	Weak transcription	Brain Germinal Matrix	brain
22	chr1:10536400-10553000	Weak transcription	Psoas Muscle	Psoas
23	chr1:10536400-10554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:10536400-10554600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:10536400-10554800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:10536400-10554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:10536400-10554800	Weak transcription	Fetal Brain Male	brain
28	chr1:10536400-10554800	Weak transcription	NHDF-Ad	bronchial
29	chr1:10536400-10555000	Weak transcription	Fetal Kidney	kidney
30	chr1:10536400-10555000	Weak transcription	HSMM	muscle
31	chr1:10536600-10540800	Weak transcription	Fetal Heart	heart
32	chr1:10536600-10544600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:10536600-10548200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:10536600-10549400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:10536600-10549400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:10536600-10549400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:10536600-10549400	Weak transcription	Fetal Lung	lung
38	chr1:10536600-10549400	Weak transcription	GM12878-XiMat	blood
39	chr1:10536600-10549400	Weak transcription	Hela-S3	cervix
40	chr1:10536600-10549600	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:10536600-10549800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:10536600-10550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:10536600-10550000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:10536600-10550200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:10536600-10550200	Weak transcription	Brain Anterior Caudate	brain
46	chr1:10536600-10554800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:10536600-10555000	Weak transcription	Brain Substantia Nigra	brain
48	chr1:10536800-10541400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:10536800-10544400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:10536800-10549400	Weak transcription	Fetal Muscle Trunk	muscle

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