Variant report

Variant	rs11693427
Chromosome Location	chr2:99763326-99763327
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	chr2:99762915..99768009-chr2:99769933..99773290,6	K562	blood:
2	chr2:99763174..99765422-chr2:99765700..99768337,2	K562	blood:

Variant related genes	Relation type
ENSG00000135951	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000144182	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10165534	0.81[ASN][1000 genomes]
rs10179043	0.83[ASN][1000 genomes]
rs10196680	0.81[ASN][1000 genomes]
rs1044575	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865029	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11123761	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11123762	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123763	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123764	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123765	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123766	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123770	0.81[EUR][1000 genomes]
rs1133977	0.83[EUR][1000 genomes]
rs1133978	0.83[EUR][1000 genomes]
rs11677247	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11677321	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11678456	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11683107	0.84[EUR][1000 genomes]
rs11683188	0.82[EUR][1000 genomes]
rs11684507	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11684610	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11685759	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11688004	0.82[EUR][1000 genomes]
rs11689265	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11692336	0.83[EUR][1000 genomes]
rs11692699	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11695379	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11695751	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11883676	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11890338	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11895749	0.83[EUR][1000 genomes]
rs11900670	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12467679	0.81[ASN][1000 genomes]
rs12473029	0.83[ASN][1000 genomes]
rs12477754	0.81[ASN][1000 genomes]
rs12477978	0.86[ASN][1000 genomes]
rs12613624	0.82[EUR][1000 genomes]
rs12619780	0.82[EUR][1000 genomes]
rs12621007	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12987548	0.81[EUR][1000 genomes]
rs12992218	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12992930	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12995473	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12999417	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13000731	0.83[EUR][1000 genomes]
rs13004491	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13008171	0.83[EUR][1000 genomes]
rs13008496	0.81[AFR][1000 genomes]
rs13009147	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13012481	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13018891	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13020339	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13022329	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13023479	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13023501	0.81[EUR][1000 genomes]
rs13023744	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13026928	0.85[EUR][1000 genomes]
rs13030961	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13033012	0.83[EUR][1000 genomes]
rs13035311	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1349778	0.81[ASN][1000 genomes]
rs1349779	0.83[ASN][1000 genomes]
rs13798	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1453563	0.82[EUR][1000 genomes]
rs1580068	0.81[ASN][1000 genomes]
rs17708218	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17759607	0.82[EUR][1000 genomes]
rs1993230	0.84[ASN][1000 genomes]
rs2045057	0.84[ASN][1000 genomes]
rs2171359	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2171362	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2309524	0.84[ASN][1000 genomes]
rs2309581	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2516827	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516828	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516829	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516830	0.84[EUR][1000 genomes]
rs2516832	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516833	0.84[EUR][1000 genomes]
rs2516834	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516835	0.85[EUR][1000 genomes]
rs2516836	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2632260	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632261	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2632277	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632283	0.85[EUR][1000 genomes]
rs2632284	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964969	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2969379	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34252185	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34272114	0.82[EUR][1000 genomes]
rs34766932	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35461437	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs36071868	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4340581	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4347885	0.82[EUR][1000 genomes]
rs4402818	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4588238	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4622780	0.81[ASN][1000 genomes]
rs4850897	0.84[EUR][1000 genomes]
rs4851187	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851188	0.82[EUR][1000 genomes]
rs6542858	0.81[ASN][1000 genomes]
rs6542863	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542864	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542865	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6542866	0.85[EUR][1000 genomes]
rs6542868	0.84[EUR][1000 genomes]
rs6542869	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542870	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6704766	0.81[ASN][1000 genomes]
rs6708576	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6708878	0.84[EUR][1000 genomes]
rs6712704	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6717723	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717729	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726618	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6727749	0.84[EUR][1000 genomes]
rs6736064	0.81[ASN][1000 genomes]
rs6739579	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6741773	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6743355	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6751927	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6753063	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6753650	0.82[AFR][1000 genomes]
rs6756650	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6757661	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6759354	0.81[ASN][1000 genomes]
rs720228	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs720229	0.81[EUR][1000 genomes]
rs7349217	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7558004	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7558239	0.84[ASN][1000 genomes]
rs7572660	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7577477	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7584809	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7604557	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7605843	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7608938	0.84[EUR][1000 genomes]
rs8179690	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs896886	0.81[ASN][1000 genomes]
rs9308816	0.81[ASN][1000 genomes]
rs972768	0.84[ASN][1000 genomes]
rs9941561	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11693427	TSGA10	cis	Thyroid	GTEx
rs11693427	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs11693427	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11693427	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs11693427	TSGA10	cis	lung	GTEx
rs11693427	TSGA10	cis	Esophagus Mucosa	GTEx
rs11693427	MITD1	cis	Nerve Tibial	GTEx
rs11693427	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99758600-99764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99758600-99770200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:99758600-99770400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:99758600-99770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:99758600-99770600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:99758600-99770600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:99758800-99769600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:99758800-99770000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:99758800-99770200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:99758800-99770200	Weak transcription	Fetal Brain Female	brain
11	chr2:99758800-99770400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:99758800-99770600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:99759000-99764200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:99759000-99767600	Weak transcription	Primary B cells from cord blood	blood
15	chr2:99759000-99769000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:99759000-99769400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:99759000-99769400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:99759000-99769600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:99759000-99769600	Weak transcription	Brain Angular Gyrus	brain
20	chr2:99759000-99769600	Weak transcription	Thymus	Thymus
21	chr2:99759000-99769800	Weak transcription	Primary T cells from cord blood	blood
22	chr2:99759000-99770200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:99759000-99770200	Weak transcription	HMEC	breast
24	chr2:99759000-99770400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:99759000-99770400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:99759000-99770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:99759000-99770400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:99759000-99770400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:99759000-99770400	Weak transcription	Brain Anterior Caudate	brain
30	chr2:99759000-99770600	Weak transcription	Fetal Kidney	kidney
31	chr2:99759200-99769600	Weak transcription	Hela-S3	cervix
32	chr2:99759200-99770400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:99759200-99770400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:99759200-99770400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:99759200-99770400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:99759400-99769200	Weak transcription	HepG2	liver
37	chr2:99761000-99767000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:99761600-99763400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:99761600-99765200	Weak transcription	Fetal Intestine Small	intestine
40	chr2:99761600-99767000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:99762400-99767000	Weak transcription	Fetal Intestine Large	intestine

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