Variant report

Variant	rs7572660
Chromosome Location	chr2:99788582-99788583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99770928..99774768-chr2:99788330..99791742,4	MCF-7	breast:
2	chr2:99788049..99790012-chr2:99797215..99799580,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241962	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000144182	Chromatin interaction
ENSG00000135951	Chromatin interaction
ENSG00000185414	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10165534	0.82[ASN][1000 genomes]
rs10179043	0.84[ASN][1000 genomes]
rs10196680	0.82[ASN][1000 genomes]
rs1044575	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865029	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123761	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123762	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11123763	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123764	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123765	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123766	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123770	0.84[EUR][1000 genomes]
rs1133977	0.84[EUR][1000 genomes]
rs1133978	0.84[EUR][1000 genomes]
rs11674894	0.82[EUR][1000 genomes]
rs11677247	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11677321	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678456	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11683107	0.85[EUR][1000 genomes]
rs11683188	0.84[EUR][1000 genomes]
rs11684507	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11684610	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11685759	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688004	0.84[EUR][1000 genomes]
rs11689265	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11692336	0.84[EUR][1000 genomes]
rs11692699	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11693427	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11695379	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11695751	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11883676	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890338	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11895749	0.84[EUR][1000 genomes]
rs11900670	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12467679	0.82[ASN][1000 genomes]
rs12473029	0.81[ASN][1000 genomes]
rs12477754	0.82[ASN][1000 genomes]
rs12613624	0.84[EUR][1000 genomes]
rs12619780	0.83[EUR][1000 genomes]
rs12621007	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12987548	0.82[EUR][1000 genomes]
rs12991189	0.80[EUR][1000 genomes]
rs12992218	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12992930	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12995473	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12999417	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13000731	0.87[EUR][1000 genomes]
rs13004491	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13008171	0.84[EUR][1000 genomes]
rs13008496	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13009147	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13012481	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13018891	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13020339	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13022329	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13023479	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13023501	0.82[EUR][1000 genomes]
rs13023744	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13026928	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13030961	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13033012	0.87[EUR][1000 genomes]
rs13035311	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1349778	0.82[ASN][1000 genomes]
rs1349779	0.81[ASN][1000 genomes]
rs13798	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453563	0.84[EUR][1000 genomes]
rs1580068	0.82[ASN][1000 genomes]
rs17708218	0.85[ASN][1000 genomes]
rs17759607	0.84[EUR][1000 genomes]
rs1993230	0.85[ASN][1000 genomes]
rs2045057	0.85[ASN][1000 genomes]
rs2171359	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171362	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2309524	0.85[ASN][1000 genomes]
rs2309581	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516827	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516828	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516829	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516830	0.85[EUR][1000 genomes]
rs2516832	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516833	0.85[EUR][1000 genomes]
rs2516834	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2516835	0.86[EUR][1000 genomes]
rs2516836	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2632260	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2632261	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632277	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2632283	0.86[EUR][1000 genomes]
rs2632284	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964969	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2969379	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34252185	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34272114	0.84[EUR][1000 genomes]
rs34766932	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35461437	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36071868	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4340581	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4347885	0.86[EUR][1000 genomes]
rs4402818	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4588238	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4622780	0.82[ASN][1000 genomes]
rs4850897	0.85[EUR][1000 genomes]
rs4851187	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851188	0.83[EUR][1000 genomes]
rs6542858	0.82[ASN][1000 genomes]
rs6542863	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542864	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542865	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542866	0.86[EUR][1000 genomes]
rs6542868	0.87[EUR][1000 genomes]
rs6542869	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542870	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704766	0.82[ASN][1000 genomes]
rs6708576	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708878	0.87[EUR][1000 genomes]
rs6712704	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6717723	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6717729	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726618	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727749	0.87[EUR][1000 genomes]
rs6736064	0.82[ASN][1000 genomes]
rs6739579	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6741773	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6743355	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6751927	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6753063	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753650	0.88[EUR][1000 genomes]
rs6756650	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757661	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759354	0.82[ASN][1000 genomes]
rs720228	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs720229	0.83[EUR][1000 genomes]
rs7349217	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558004	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577477	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584809	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7604557	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7605843	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608938	0.87[EUR][1000 genomes]
rs8179690	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896886	0.82[ASN][1000 genomes]
rs9308816	0.82[ASN][1000 genomes]
rs972768	0.85[ASN][1000 genomes]
rs9941561	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7572660	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs7572660	MITD1	cis	Esophagus Mucosa	GTEx
rs7572660	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs7572660	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs7572660	TSGA10	cis	Esophagus Mucosa	GTEx
rs7572660	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs7572660	TSGA10	cis	multi-tissue	Pritchard
rs7572660	TSGA10	cis	lung	GTEx
rs7572660	MITD1	cis	Nerve Tibial	GTEx
rs7572660	TSGA10	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99772200-99795600	Weak transcription	Gastric	stomach
2	chr2:99772400-99795600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:99772400-99795600	Weak transcription	Small Intestine	intestine
4	chr2:99772400-99796400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:99772400-99796600	Weak transcription	Right Ventricle	heart
6	chr2:99772400-99796800	Weak transcription	Colonic Mucosa	Colon
7	chr2:99772400-99797000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:99772600-99795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:99772600-99796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:99772600-99796600	Weak transcription	Fetal Kidney	kidney
11	chr2:99772600-99797000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:99772800-99796400	Weak transcription	Fetal Heart	heart
13	chr2:99773000-99796400	Weak transcription	Fetal Brain Male	brain
14	chr2:99773200-99790800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:99773600-99790400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:99774000-99796200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:99774600-99795400	Weak transcription	K562	blood
18	chr2:99775000-99795600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:99775200-99788600	Weak transcription	Fetal Intestine Small	intestine
20	chr2:99775200-99790400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:99775400-99795400	Weak transcription	Brain Substantia Nigra	brain
22	chr2:99775800-99790400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:99776400-99795600	Weak transcription	Fetal Lung	lung
24	chr2:99776600-99795200	Weak transcription	Brain Angular Gyrus	brain
25	chr2:99779400-99795600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:99780400-99790400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:99780600-99790400	Strong transcription	Dnd41	blood
28	chr2:99780600-99791000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:99780800-99791000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr2:99781000-99789800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:99781000-99790400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:99781000-99790400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:99781000-99790400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:99781000-99790800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:99781000-99790800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:99781200-99788600	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:99781200-99790400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:99781200-99790400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:99781200-99791000	Strong transcription	Fetal Thymus	thymus
40	chr2:99781400-99790400	Strong transcription	Adipose Nuclei	Adipose
41	chr2:99781600-99790400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr2:99781600-99790400	Strong transcription	Primary hematopoietic stem cells	blood
43	chr2:99781600-99790400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr2:99781600-99791000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:99781800-99790200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:99781800-99790200	Strong transcription	Primary B cells from cord blood	blood
47	chr2:99781800-99790400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:99781800-99790400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:99781800-99790400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:99781800-99790400	Strong transcription	Rectal Mucosa Donor 31	rectum

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