Variant report

Variant	rs10912746
Chromosome Location	chr1:174179343-174179344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174178623..174180294-chr1:174184610..174187215,2	K562	blood:
2	chr1:174178345..174180252-chr1:174182223..174184373,2	K562	blood:
3	chr1:174128679..174131569-chr1:174177362..174180012,2	K562	blood:

Variant related genes	Relation type
ENSG00000152061	Chromatin interaction
ENSG00000227373	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10798307	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10798308	0.85[ASN][1000 genomes]
rs10798309	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798311	0.81[EUR][1000 genomes]
rs10912728	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10912733	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10912735	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10912737	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10912740	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10912741	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10912747	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912750	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912751	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912753	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912754	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912757	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10912758	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10912759	0.84[ASN][1000 genomes]
rs10912762	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10912774	0.81[EUR][1000 genomes]
rs10912782	0.81[EUR][1000 genomes]
rs1121537	0.84[ASN][1000 genomes]
rs11802158	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807537	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12059434	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12060460	0.84[ASN][1000 genomes]
rs12065785	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12066504	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12066700	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12067852	0.84[ASN][1000 genomes]
rs12072050	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12074107	0.84[ASN][1000 genomes]
rs12074276	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12076453	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076771	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12079214	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12079687	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12079689	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080977	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081445	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082461	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12083540	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12083814	0.84[ASN][1000 genomes]
rs12085311	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12087808	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12091012	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12091155	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12091157	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12093691	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12097252	0.91[AFR][1000 genomes]
rs12354141	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1407127	0.82[EUR][1000 genomes]
rs1417186	0.86[EUR][1000 genomes]
rs1591944	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16846717	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16846718	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16846816	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846938	0.81[EUR][1000 genomes]
rs17300775	0.86[EUR][1000 genomes]
rs17350956	0.82[EUR][1000 genomes]
rs17350991	0.81[EUR][1000 genomes]
rs17353198	0.81[EUR][1000 genomes]
rs1934681	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2103640	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142863	0.84[ASN][1000 genomes]
rs2142864	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2142865	0.84[ASN][1000 genomes]
rs2860907	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860909	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3086	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4233169	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4233171	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4607949	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650950	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4650951	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4650958	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4650959	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4650968	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650969	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650981	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652179	0.82[EUR][1000 genomes]
rs4652191	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4652193	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4652204	0.84[EUR][1000 genomes]
rs4652275	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55698100	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56152378	0.82[EUR][1000 genomes]
rs56158362	0.86[EUR][1000 genomes]
rs56239105	0.86[EUR][1000 genomes]
rs56338048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375942	0.86[EUR][1000 genomes]
rs56404641	0.86[EUR][1000 genomes]
rs57407575	0.82[EUR][1000 genomes]
rs59044210	0.84[EUR][1000 genomes]
rs59649440	0.92[EUR][1000 genomes]
rs61528155	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425277	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425278	0.84[ASN][1000 genomes]
rs6656491	0.82[EUR][1000 genomes]
rs6666588	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668008	0.84[EUR][1000 genomes]
rs6670425	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6676161	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6678209	0.89[AFR][1000 genomes]
rs6678286	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685499	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6692437	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693198	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6694208	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6697959	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6700482	0.84[ASN][1000 genomes]
rs724888	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs724889	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72711443	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72711457	0.82[EUR][1000 genomes]
rs72711487	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72711492	0.85[EUR][1000 genomes]
rs72711501	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713503	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713504	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713505	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs727912	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7535987	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7536987	0.81[EUR][1000 genomes]
rs7551605	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553317	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10912746	RP11-160H22.5	cis	Thyroid	GTEx
rs10912746	MRPS14	Cis_1M	lymphoblastoid	RTeQTL
rs10912746	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174160800-174186600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:174162000-174189600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:174172200-174179800	ZNF genes & repeats	GM12878-XiMat	blood
4	chr1:174172800-174190600	Weak transcription	Fetal Intestine Large	intestine
5	chr1:174172800-174191000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:174173200-174191400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:174174000-174186200	Weak transcription	Ovary	ovary
8	chr1:174174200-174180200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:174174200-174200200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:174175400-174200200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:174176000-174190800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:174176000-174222400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:174176200-174188800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:174176200-174191200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:174176800-174189400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:174176800-174222400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:174177000-174191200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:174177200-174212000	Weak transcription	Lung	lung
19	chr1:174178000-174179400	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr1:174178000-174179400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr1:174178400-174179400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:174178400-174179800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:174178600-174179400	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr1:174178600-174179400	ZNF genes & repeats	K562	blood
25	chr1:174178600-174179600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:174178600-174212200	Weak transcription	Psoas Muscle	Psoas
27	chr1:174178800-174190800	Weak transcription	Thymus	Thymus
28	chr1:174179000-174179400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:174179000-174180000	Weak transcription	Esophagus	oesophagus
30	chr1:174179000-174186600	Weak transcription	Left Ventricle	heart
31	chr1:174179200-174179400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr1:174179200-174180000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr1:174179200-174190800	Weak transcription	Dnd41	blood

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