Variant report

Variant	rs11677462
Chromosome Location	chr2:231309404-231309405
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr2:231309335-231309871	GM12878	blood:	n/a	n/a
2	RUNX3	chr2:231309385-231309925	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:231309089-231309656	GM12892	blood:	n/a	n/a
4	POLR2A	chr2:231309155-231309858	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:231309048-231309836	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:231309077-231310154	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:231309332-231309571	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:231309182-231309676	GM12891	blood:	n/a	n/a
9	POLR2A	chr2:231309223-231309756	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
SP100	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1074886	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11675127	0.87[ASN][1000 genomes]
rs11675135	0.87[ASN][1000 genomes]
rs11676089	0.87[ASN][1000 genomes]
rs11676310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677646	0.85[ASN][1000 genomes]
rs11679026	0.85[ASN][1000 genomes]
rs11681234	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11681358	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11687964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688362	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11688458	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11692506	1.00[JPT][hapmap]
rs11692527	0.87[ASN][1000 genomes]
rs11692602	0.87[ASN][1000 genomes]
rs11693767	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11694346	0.93[ASN][1000 genomes]
rs11694422	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11694428	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694865	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1427284	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17273079	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17332171	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17332742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17333189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303608	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35919859	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3752431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3754940	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3754941	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3754942	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3754943	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769849	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3815885	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893836	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs55637456	0.93[ASN][1000 genomes]
rs55770359	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893188	0.85[ASN][1000 genomes]
rs55964110	0.87[ASN][1000 genomes]
rs56007282	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044062	0.87[ASN][1000 genomes]
rs56052963	0.87[ASN][1000 genomes]
rs56105857	0.87[ASN][1000 genomes]
rs56108366	0.87[ASN][1000 genomes]
rs56251216	0.87[ASN][1000 genomes]
rs56303947	0.87[ASN][1000 genomes]
rs56372741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56401027	0.85[ASN][1000 genomes]
rs6436933	0.87[ASN][1000 genomes]
rs6706167	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6713447	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6713465	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6722656	0.90[ASN][1000 genomes]
rs6725726	0.90[ASN][1000 genomes]
rs6732684	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6732940	0.87[ASN][1000 genomes]
rs6748339	0.87[ASN][1000 genomes]
rs6748445	0.87[ASN][1000 genomes]
rs6750712	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753500	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6759292	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761255	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs68096532	0.93[ASN][1000 genomes]
rs72495174	0.87[ASN][1000 genomes]
rs72495175	0.87[ASN][1000 genomes]
rs72495176	0.87[ASN][1000 genomes]
rs72495180	0.87[ASN][1000 genomes]
rs72495181	0.87[ASN][1000 genomes]
rs72495182	0.87[ASN][1000 genomes]
rs72495183	0.93[ASN][1000 genomes]
rs72495185	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725202	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs72994332	0.85[ASN][1000 genomes]
rs72996270	0.85[ASN][1000 genomes]
rs72996292	0.87[ASN][1000 genomes]
rs72998203	0.87[ASN][1000 genomes]
rs72998264	0.93[ASN][1000 genomes]
rs72998283	0.93[ASN][1000 genomes]
rs73000239	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000253	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000268	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559665	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7563909	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7568128	0.93[ASN][1000 genomes]
rs7585646	0.87[ASN][1000 genomes]
rs7585731	0.87[ASN][1000 genomes]
rs7589948	0.87[ASN][1000 genomes]
rs7597033	0.87[ASN][1000 genomes]
rs7606804	0.93[ASN][1000 genomes]
rs999888	1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv584672	chr2:231289976-231348888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11677462	LOC93349	Cis_1M	lymphoblastoid	RTeQTL
rs11677462	SP140L	cis	Nerve Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231288800-231319000	Weak transcription	Fetal Kidney	kidney
2	chr2:231288800-231356000	Weak transcription	Stomach Mucosa	stomach
3	chr2:231294200-231309600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:231294200-231311600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:231296000-231310400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:231301400-231314400	Weak transcription	Psoas Muscle	Psoas
7	chr2:231301800-231312000	Weak transcription	HepG2	liver
8	chr2:231301800-231345000	Weak transcription	A549	lung
9	chr2:231303200-231317200	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr2:231304400-231320800	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:231306000-231314400	Weak transcription	Esophagus	oesophagus
12	chr2:231306600-231310400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:231306600-231312000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:231306600-231323400	Weak transcription	K562	blood
15	chr2:231306800-231311600	Genic enhancers	GM12878-XiMat	blood
16	chr2:231306800-231311800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:231306800-231318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:231307400-231312600	Genic enhancers	Primary B cells from cord blood	blood
19	chr2:231307400-231317600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:231307400-231318200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:231307400-231321800	Strong transcription	Liver	Liver
22	chr2:231307600-231309600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:231307600-231311400	Strong transcription	Thymus	Thymus
24	chr2:231307600-231311600	Weak transcription	Hela-S3	cervix
25	chr2:231307600-231311800	Strong transcription	Fetal Thymus	thymus
26	chr2:231307600-231312200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:231307600-231312400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:231307600-231315000	Strong transcription	Fetal Muscle Leg	muscle
29	chr2:231307600-231315000	Strong transcription	Left Ventricle	heart
30	chr2:231307600-231315400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:231307600-231316600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr2:231307600-231318200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr2:231307600-231319600	Strong transcription	Dnd41	blood
34	chr2:231307600-231336600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:231307800-231309600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:231307800-231309600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:231307800-231309600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:231307800-231315000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:231307800-231315000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:231307800-231315200	Strong transcription	HSMMtube	muscle
41	chr2:231307800-231318400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:231308000-231311400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:231308000-231311600	Strong transcription	Primary T cells from cord blood	blood
44	chr2:231308000-231312200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:231308000-231312600	Strong transcription	Adipose Nuclei	Adipose
46	chr2:231308000-231314000	Weak transcription	Brain Substantia Nigra	brain
47	chr2:231308000-231315000	Strong transcription	Fetal Intestine Small	intestine
48	chr2:231308000-231315200	Strong transcription	HSMM	muscle
49	chr2:231308000-231315800	Strong transcription	Placenta	Placenta
50	chr2:231308200-231311200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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