Variant report

Variant	rs56338048
Chromosome Location	chr1:174189404-174189405
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	STAT3	chr1:174189122-174189460	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:174189133-174189499	MCF10A-Er-Src	breast:	n/a	n/a
3	NFIC	chr1:174188699-174189483	GM12878	blood:	n/a	chr1:174189334-174189350 chr1:174189333-174189350
4	FOS	chr1:174189106-174189483	MCF10A-Er-Src	breast:	n/a	chr1:174189290-174189301 chr1:174189312-174189321 chr1:174189292-174189303
5	FOS	chr1:174189101-174189459	HUVEC	blood vessel:	n/a	chr1:174189290-174189301 chr1:174189312-174189321 chr1:174189292-174189303
6	FOS	chr1:174189134-174189459	MCF10A-Er-Src	breast:	n/a	chr1:174189290-174189301 chr1:174189312-174189321 chr1:174189292-174189303
7	STAT3	chr1:174189129-174189442	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:174189120-174189455	MCF10A-Er-Src	breast:	n/a	chr1:174189290-174189301 chr1:174189312-174189321 chr1:174189292-174189303

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174188636..174191430-chr1:174968395..174970624,2	K562	blood:

Variant related genes	Relation type
RABGAP1L	TF binding region
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 136 )
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]
rs10912746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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]
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:10 , 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
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56338048	RP11-160H22.5	cis	Thyroid	GTEx
rs56338048	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs56338048	MRPS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174162000-174189600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:174172800-174190600	Weak transcription	Fetal Intestine Large	intestine
3	chr1:174172800-174191000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:174173200-174191400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:174174200-174200200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:174175400-174200200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:174176000-174190800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:174176000-174222400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:174176200-174191200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:174176800-174222400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:174177000-174191200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:174177200-174212000	Weak transcription	Lung	lung
13	chr1:174178600-174212200	Weak transcription	Psoas Muscle	Psoas
14	chr1:174178800-174190800	Weak transcription	Thymus	Thymus
15	chr1:174179200-174190800	Weak transcription	Dnd41	blood
16	chr1:174179400-174190200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:174179400-174191000	Weak transcription	Fetal Intestine Small	intestine
18	chr1:174186200-174191200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:174186400-174189600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:174186600-174190400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:174186600-174191400	Weak transcription	Fetal Kidney	kidney
22	chr1:174186600-174216600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:174186800-174190400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:174186800-174190800	Weak transcription	Left Ventricle	heart
25	chr1:174186800-174191000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:174186800-174191000	Weak transcription	Aorta	Aorta
27	chr1:174186800-174191200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:174186800-174191400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:174186800-174191400	Weak transcription	Adipose Nuclei	Adipose
30	chr1:174186800-174200400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:174186800-174200600	Weak transcription	Fetal Stomach	stomach
32	chr1:174186800-174200600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:174186800-174208000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:174186800-174212800	Weak transcription	Fetal Heart	heart
35	chr1:174186800-174213200	Weak transcription	Ovary	ovary
36	chr1:174186800-174217000	Weak transcription	Brain Angular Gyrus	brain
37	chr1:174186800-174232000	Weak transcription	HSMMtube	muscle
38	chr1:174187000-174191200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:174187000-174199600	Weak transcription	A549	lung
40	chr1:174187000-174217000	Weak transcription	Pancreas	Pancrea
41	chr1:174187200-174190200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:174187200-174190800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:174187400-174190400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:174187400-174191000	Weak transcription	Osteobl	bone
45	chr1:174187400-174191200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:174187400-174200400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:174187400-174208000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:174187600-174190200	Weak transcription	K562	blood
49	chr1:174187600-174190400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:174187600-174190800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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