Variant report

Variant	rs7558004
Chromosome Location	chr2:99808795-99808796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99808671..99811447-chr2:99812469..99815552,3	K562	blood:
2	chr2:99771094..99773353-chr2:99808204..99810029,2	K562	blood:
3	chr2:99803346..99805828-chr2:99808028..99810018,2	MCF-7	breast:
4	chr2:99796625..99803903-chr2:99808531..99815139,9	K562	blood:
5	chr2:99796728..99798247-chr2:99808341..99810183,2	K562	blood:
6	chr2:99808671..99812462-chr2:99812469..99815885,5	K562	blood:

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

Extended variants
information (count: 147 )
Associated
traits (count: 7 )

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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865029	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123761	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123762	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11123763	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123764	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123765	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123766	0.94[AMR][1000 genomes];0.97[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	0.81[EUR][1000 genomes]
rs11677247	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11677321	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678456	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11683107	0.85[EUR][1000 genomes]
rs11683188	0.83[EUR][1000 genomes]
rs11684507	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11684610	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11685759	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688004	0.83[EUR][1000 genomes]
rs11689265	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11692336	0.84[EUR][1000 genomes]
rs11692699	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11693427	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11695379	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11695751	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11883676	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890338	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11895749	0.84[EUR][1000 genomes]
rs11900670	0.89[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	0.83[EUR][1000 genomes]
rs12619780	0.83[EUR][1000 genomes]
rs12621007	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12987548	0.82[EUR][1000 genomes]
rs12992218	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12992930	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12995473	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12999417	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13000731	0.86[EUR][1000 genomes]
rs13004491	0.92[AMR][1000 genomes];0.93[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	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13012481	0.86[EUR][1000 genomes]
rs13018891	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13020339	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13022329	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13023479	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13023501	0.82[EUR][1000 genomes]
rs13023744	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13025880	0.86[AFR][1000 genomes]
rs13026928	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13030961	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13033012	0.86[EUR][1000 genomes]
rs13035311	0.89[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	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453563	0.83[EUR][1000 genomes]
rs1580068	0.82[ASN][1000 genomes]
rs17708218	0.85[ASN][1000 genomes]
rs17759607	0.83[EUR][1000 genomes]
rs1993230	0.85[ASN][1000 genomes]
rs2045057	0.85[ASN][1000 genomes]
rs2171359	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171362	0.89[EUR][1000 genomes]
rs2309524	0.85[ASN][1000 genomes]
rs2309581	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516827	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516828	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516829	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516830	0.85[EUR][1000 genomes]
rs2516832	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516833	0.85[EUR][1000 genomes]
rs2516834	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2516835	0.86[EUR][1000 genomes]
rs2516836	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2632260	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2632261	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632277	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2632283	0.86[EUR][1000 genomes]
rs2632284	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964969	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2969379	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34252185	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34272114	0.83[EUR][1000 genomes]
rs34766932	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35461437	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36071868	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4340581	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4347885	0.85[EUR][1000 genomes]
rs4402818	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4588238	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4622780	0.82[ASN][1000 genomes]
rs4850897	0.85[EUR][1000 genomes]
rs4851187	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851188	0.83[EUR][1000 genomes]
rs6542858	0.82[ASN][1000 genomes]
rs6542863	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542864	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542865	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542866	0.86[EUR][1000 genomes]
rs6542868	0.87[EUR][1000 genomes]
rs6542869	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542870	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704766	0.82[ASN][1000 genomes]
rs6708576	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708878	0.87[EUR][1000 genomes]
rs6712704	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6717723	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6717729	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726618	0.86[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	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6741773	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6743355	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6751927	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6753063	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753650	0.87[EUR][1000 genomes]
rs6756650	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757661	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759354	0.82[ASN][1000 genomes]
rs720228	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs720229	0.82[EUR][1000 genomes]
rs7349217	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572660	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577477	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584809	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7604557	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7605843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608938	0.87[EUR][1000 genomes]
rs8179690	0.98[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	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7558004	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs7558004	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs7558004	TSGA10	cis	Esophagus Mucosa	GTEx
rs7558004	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs7558004	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs7558004	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs7558004	TSGA10	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798400-99812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:99798600-99812000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:99798600-99812000	Weak transcription	Aorta	Aorta
4	chr2:99798600-99814000	Weak transcription	Right Ventricle	heart
5	chr2:99798600-99814800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:99798600-99815200	Weak transcription	Esophagus	oesophagus
7	chr2:99798600-99822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
9	chr2:99798800-99810800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:99798800-99812000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:99798800-99812000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:99798800-99812000	Weak transcription	Fetal Kidney	kidney
13	chr2:99798800-99815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
15	chr2:99799200-99811800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:99799200-99813000	Weak transcription	HUVEC	blood vessel
17	chr2:99799200-99824200	Weak transcription	Fetal Brain Male	brain
18	chr2:99799600-99811200	Weak transcription	HMEC	breast
19	chr2:99799600-99812600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:99799600-99814200	Weak transcription	NHLF	lung
21	chr2:99799800-99811000	Weak transcription	Osteobl	bone
22	chr2:99799800-99812000	Weak transcription	Gastric	stomach
23	chr2:99799800-99814400	Weak transcription	Brain Angular Gyrus	brain
24	chr2:99799800-99816800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:99800000-99812000	Weak transcription	Lung	lung
26	chr2:99800400-99816400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:99801600-99812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:99801600-99812600	Weak transcription	Pancreas	Pancrea
29	chr2:99802600-99809200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:99802600-99809400	Strong transcription	Liver	Liver
31	chr2:99802600-99817000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:99802800-99809000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:99802800-99809000	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:99803000-99809000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:99803000-99809200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:99803000-99814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:99803000-99814400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:99803000-99815200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:99803000-99815800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:99803000-99818400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:99803200-99809000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:99803200-99809000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:99803400-99809000	Strong transcription	Primary B cells from cord blood	blood
44	chr2:99803400-99809000	Strong transcription	Primary T cells from cord blood	blood
45	chr2:99803400-99809000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:99803400-99809000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:99803400-99809000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:99803400-99809000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:99803400-99809200	Strong transcription	Fetal Thymus	thymus
50	chr2:99803400-99815200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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