Variant report

Variant	rs10801620
Chromosome Location	chr1:197591406-197591407
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197583946..197585840-chr1:197589474..197591778,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10754228	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10922231	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs10922236	0.82[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10922252	0.85[ASN][1000 genomes]
rs10922259	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10922260	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10922266	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1135810	0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs12042609	0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs12066841	0.88[ASN][1000 genomes]
rs12081207	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs1345529	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1923759	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs1998711	0.96[ASN][1000 genomes]
rs2111930	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111934	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4026508	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4026513	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4026514	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs4274099	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4282851	1.00[ASN][1000 genomes]
rs4611052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915561	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap]
rs55995691	0.86[ASN][1000 genomes]
rs6428416	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6667685	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6675292	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs6688289	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6691216	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7516153	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7516334	0.84[ASN][1000 genomes]
rs7516481	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs7523627	0.95[ASN][1000 genomes]
rs7533766	0.89[ASN][1000 genomes]
rs7534863	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7548454	1.00[ASN][1000 genomes]
rs9633354	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9787082	0.82[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv548872	chr1:197529218-197644581	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3397065	chr1:197545083-197637033	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10801620	LHX2	trans	parietal	SCAN
rs10801620	DENND1B	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197508400-197602400	Weak transcription	Left Ventricle	heart
2	chr1:197537400-197602200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:197541800-197602400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:197541800-197602600	Weak transcription	Fetal Thymus	thymus
5	chr1:197542000-197609000	Weak transcription	Colonic Mucosa	Colon
6	chr1:197542000-197626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:197544400-197602400	Weak transcription	Primary B cells from cord blood	blood
8	chr1:197547400-197602400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:197553000-197629800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:197564800-197599200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:197564800-197599400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:197565000-197611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:197578600-197611000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:197579000-197599000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:197579400-197599000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:197581000-197602600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:197583800-197599000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:197584800-197602600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:197586000-197609800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:197586400-197594600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:197586400-197602000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:197586800-197599000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:197586800-197599000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:197587000-197599000	Weak transcription	Primary T cells from cord blood	blood
25	chr1:197587000-197602400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:197587000-197609800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:197587200-197602400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:197587400-197594400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:197587400-197606600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:197587600-197599000	Weak transcription	Dnd41	blood
31	chr1:197587600-197602400	Weak transcription	Fetal Lung	lung
32	chr1:197587600-197610800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:197588600-197602200	Weak transcription	Fetal Heart	heart
34	chr1:197590000-197613400	Weak transcription	Stomach Mucosa	stomach
35	chr1:197590200-197599000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:197590400-197592000	Enhancers	Liver	Liver
37	chr1:197590400-197592000	Enhancers	HepG2	liver
38	chr1:197590400-197602600	Weak transcription	Pancreas	Pancrea
39	chr1:197591000-197591600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:197591400-197591800	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:197591400-197591800	Enhancers	Fetal Intestine Large	intestine

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