Variant report

Variant	rs11555142
Chromosome Location	chr7:99032593-99032594
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	chr7:99030944..99035080-chr7:99035226..99039444,6	MCF-7	breast:
2	chr7:99004079..99005950-chr7:99029849..99032633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10215765	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215854	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226310	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229886	1.00[ASN][1000 genomes]
rs10230784	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235235	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236240	1.00[ASN][1000 genomes]
rs10240199	0.86[EUR][1000 genomes]
rs10264505	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265385	0.86[EUR][1000 genomes]
rs10268984	1.00[ASN][1000 genomes]
rs10273424	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275381	1.00[ASN][1000 genomes]
rs10277447	1.00[ASN][1000 genomes]
rs10808111	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10808112	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953288	1.00[ASN][1000 genomes]
rs10953289	1.00[ASN][1000 genomes]
rs11761528	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766423	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971640	1.00[ASN][1000 genomes]
rs11973173	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973801	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974593	1.00[ASN][1000 genomes]
rs11978345	1.00[ASN][1000 genomes]
rs11978582	1.00[ASN][1000 genomes]
rs11980143	1.00[ASN][1000 genomes]
rs11980995	1.00[ASN][1000 genomes]
rs11980999	1.00[ASN][1000 genomes]
rs11983474	1.00[ASN][1000 genomes]
rs12531852	1.00[ASN][1000 genomes]
rs12533251	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535424	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536002	1.00[ASN][1000 genomes]
rs12539480	1.00[ASN][1000 genomes]
rs13223272	1.00[ASN][1000 genomes]
rs13227522	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243267	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161687	1.00[ASN][1000 genomes]
rs17161761	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003498	1.00[ASN][1000 genomes]
rs28371764	1.00[ASN][1000 genomes]
rs28419687	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602855	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627543	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096782	1.00[ASN][1000 genomes]
rs34111611	1.00[ASN][1000 genomes]
rs34257469	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183025	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35296070	1.00[ASN][1000 genomes]
rs35656351	1.00[ASN][1000 genomes]
rs36104094	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45618033	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765	1.00[ASN][1000 genomes]
rs55761861	1.00[ASN][1000 genomes]
rs57786744	1.00[ASN][1000 genomes]
rs57980352	1.00[ASN][1000 genomes]
rs58964157	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60127638	1.00[ASN][1000 genomes]
rs60577432	1.00[ASN][1000 genomes]
rs61740607	1.00[ASN][1000 genomes]
rs66478766	1.00[ASN][1000 genomes]
rs66509940	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66568021	1.00[ASN][1000 genomes]
rs66674233	1.00[ASN][1000 genomes]
rs67279166	1.00[ASN][1000 genomes]
rs67309224	1.00[ASN][1000 genomes]
rs67546174	1.00[ASN][1000 genomes]
rs67860332	1.00[ASN][1000 genomes]
rs67909852	1.00[ASN][1000 genomes]
rs67934834	1.00[ASN][1000 genomes]
rs6947826	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947941	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947974	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955891	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960810	1.00[ASN][1000 genomes]
rs704798	1.00[ASN][1000 genomes]
rs73157587	1.00[ASN][1000 genomes]
rs73157588	1.00[ASN][1000 genomes]
rs73157589	1.00[ASN][1000 genomes]
rs73157590	1.00[ASN][1000 genomes]
rs73157596	1.00[ASN][1000 genomes]
rs73157600	1.00[ASN][1000 genomes]
rs73157601	1.00[ASN][1000 genomes]
rs73157602	1.00[ASN][1000 genomes]
rs73159506	1.00[ASN][1000 genomes]
rs73159509	1.00[ASN][1000 genomes]
rs73159522	1.00[ASN][1000 genomes]
rs73163167	1.00[ASN][1000 genomes]
rs73163169	1.00[ASN][1000 genomes]
rs740160	1.00[ASN][1000 genomes]
rs7778859	1.00[ASN][1000 genomes]
rs868391	1.00[ASN][1000 genomes]
rs9632722	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656060	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv888769	chr7:99018584-99041748	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv888770	chr7:99021344-99041748	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11555142	GS1-259H13.2	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99011400-99035000	Weak transcription	Fetal Brain Male	brain
3	chr7:99015600-99035200	Weak transcription	Fetal Kidney	kidney
4	chr7:99015600-99035400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:99015600-99035600	Weak transcription	Stomach Mucosa	stomach
6	chr7:99016800-99036000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:99017600-99035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:99018200-99035200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:99018200-99035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:99018400-99035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:99021400-99034400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:99021600-99035200	Weak transcription	HMEC	breast
13	chr7:99022200-99035400	Weak transcription	NH-A	brain
14	chr7:99023000-99036000	Weak transcription	Small Intestine	intestine
15	chr7:99025600-99033000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:99025600-99033000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr7:99025600-99033000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:99025600-99033000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:99025600-99033200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:99025600-99033200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:99025600-99033400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:99025600-99033400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:99025600-99033800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:99025600-99034400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:99025600-99034800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:99025600-99034800	Strong transcription	Fetal Muscle Leg	muscle
27	chr7:99025600-99035200	Strong transcription	Fetal Stomach	stomach
28	chr7:99025800-99033000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:99025800-99033200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr7:99025800-99034000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:99026000-99032800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:99026000-99032800	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:99026000-99033200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:99026200-99032800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:99026200-99032800	Strong transcription	Colonic Mucosa	Colon
36	chr7:99026200-99032800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr7:99026200-99032800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:99026200-99032800	Strong transcription	Fetal Brain Female	brain
39	chr7:99026200-99032800	Strong transcription	Fetal Thymus	thymus
40	chr7:99026200-99032800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr7:99026200-99033000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr7:99026200-99033000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:99026200-99033000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:99026200-99033000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:99026200-99033000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:99026200-99033000	Strong transcription	Adipose Nuclei	Adipose
47	chr7:99026200-99033000	Strong transcription	Brain Germinal Matrix	brain
48	chr7:99026200-99033000	Strong transcription	Brain Hippocampus Middle	brain
49	chr7:99026200-99033000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr7:99026200-99033200	Strong transcription	Primary monocytes fromperipheralblood	blood

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