Variant report

Variant	rs61826779
Chromosome Location	chr1:173966050-173966051
allele	C/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	POLR2A	chr1:173966040-173966072	H1-hESC	embryonic stem cell:	n/a	n/a
2	PAX5	chr1:173966038-173966407	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173835569..173838721-chr1:173965548..173969329,3	K562	blood:
2	chr1:173964310..173967666-chr1:173990049..173993050,6	MCF-7	breast:
3	chr1:173791607..173793893-chr1:173965038..173968720,3	K562	blood:
4	chr1:173964894..173966462-chr1:173970460..173973100,2	K562	blood:

Variant related genes	Relation type
RC3H1	TF binding region
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000120334	Chromatin interaction

Extended variants
information (count: 178 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:173)

rs_ID	r²[population]
rs10127823	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10494491	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912702	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912710	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10912716	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912717	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912721	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11489771	0.80[EUR][1000 genomes]
rs12029025	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12058585	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12060191	0.81[EUR][1000 genomes]
rs12060331	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12060401	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063266	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12063818	0.81[EUR][1000 genomes]
rs12067580	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12069129	0.89[ASN][1000 genomes]
rs12071784	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12072602	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12072905	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12077782	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12077812	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12083593	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12085939	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12086019	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12086826	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12087212	0.81[EUR][1000 genomes]
rs12089005	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12089405	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093885	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562588	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12563156	0.87[EUR][1000 genomes]
rs12564858	0.82[EUR][1000 genomes]
rs12565352	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12565675	0.81[EUR][1000 genomes]
rs12565973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566022	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12566642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566651	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12566842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1322776	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1322778	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1322779	0.80[EUR][1000 genomes]
rs13375205	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1407126	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1407596	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1407597	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16828467	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16846641	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846667	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16846688	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1890881	0.82[EUR][1000 genomes]
rs1987871	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1987872	0.85[ASN][1000 genomes]
rs1987873	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2009083	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2025241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2227588	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2227590	0.88[EUR][1000 genomes]
rs2227593	0.88[EUR][1000 genomes]
rs2227594	0.87[EUR][1000 genomes]
rs2227595	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2227597	0.88[EUR][1000 genomes]
rs2227601	0.86[EUR][1000 genomes]
rs2227612	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2295958	0.85[EUR][1000 genomes]
rs28595073	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2860841	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860845	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2901784	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36013663	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3980286	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536054	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652298	0.81[EUR][1000 genomes]
rs4652328	0.81[EUR][1000 genomes]
rs56926540	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57849055	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57995528	0.81[EUR][1000 genomes]
rs58092103	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59520434	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59960208	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60039606	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60265316	0.83[EUR][1000 genomes]
rs60551050	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61826771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826774	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61826777	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826780	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826784	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826785	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826823	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826826	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826829	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826831	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827889	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61827901	0.82[EUR][1000 genomes]
rs61827902	0.82[EUR][1000 genomes]
rs61827903	0.82[EUR][1000 genomes]
rs61827904	0.84[EUR][1000 genomes]
rs61827905	0.82[EUR][1000 genomes]
rs61827928	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61827930	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61827932	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61827933	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61827934	0.83[EUR][1000 genomes]
rs61827935	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61827936	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61827938	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61827956	0.88[EUR][1000 genomes]
rs61827957	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61827959	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828571	0.82[EUR][1000 genomes]
rs61828575	0.82[EUR][1000 genomes]
rs61828576	0.82[EUR][1000 genomes]
rs61828577	0.82[EUR][1000 genomes]
rs61828578	0.82[EUR][1000 genomes]
rs61828580	0.82[EUR][1000 genomes]
rs61828583	0.82[EUR][1000 genomes]
rs61828584	0.82[EUR][1000 genomes]
rs61828587	0.82[EUR][1000 genomes]
rs61828895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61828898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61828899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61828900	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61828901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425262	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425264	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425266	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425267	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425271	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425272	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6657380	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661182	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6665720	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6665880	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668543	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6676307	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6680088	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6683276	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6684527	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6688176	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695887	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695940	0.87[EUR][1000 genomes]
rs6698123	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6702454	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703547	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs677	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs724416	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73039035	0.87[EUR][1000 genomes]
rs7523504	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525325	0.81[EUR][1000 genomes]
rs7528380	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7530661	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7547880	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549291	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767053	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9283385	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9286896	0.88[EUR][1000 genomes]
rs9425431	0.81[EUR][1000 genomes]
rs9425433	0.81[EUR][1000 genomes]
rs9425434	0.81[EUR][1000 genomes]
rs9425436	0.86[EUR][1000 genomes]
rs9425762	0.81[EUR][1000 genomes]
rs9425773	0.81[ASN][1000 genomes]
rs9425775	0.82[ASN][1000 genomes]
rs9425779	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425780	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs961148	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965498	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9728376	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	esv3692957	chr1:173960747-173967521	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61826779	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:173901600-173966400	Strong transcription	Dnd41	blood
6	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
9	chr1:173931200-173969800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:173942200-173967400	Weak transcription	Fetal Heart	heart
11	chr1:173942200-173986200	Weak transcription	Fetal Brain Male	brain
12	chr1:173949200-173970600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:173949600-173970600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:173950600-173973400	Weak transcription	Psoas Muscle	Psoas
15	chr1:173952200-173967200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:173952800-173967600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:173953200-173974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:173955600-173966200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:173956200-173966400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:173958200-173966400	Strong transcription	Fetal Intestine Small	intestine
21	chr1:173958200-173966400	Strong transcription	Fetal Stomach	stomach
22	chr1:173958400-173967200	Weak transcription	NHLF	lung
23	chr1:173958600-173987200	Weak transcription	Gastric	stomach
24	chr1:173960400-173966400	Strong transcription	K562	blood
25	chr1:173960800-173970400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:173962000-173967400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:173962000-173967600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:173962000-173975000	Weak transcription	Right Ventricle	heart
29	chr1:173962000-173988400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:173962200-173966800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:173962200-173966800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:173962200-173966800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:173962200-173966800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:173962200-173966800	Weak transcription	A549	lung
35	chr1:173962200-173966800	Weak transcription	NHDF-Ad	bronchial
36	chr1:173962200-173967000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:173962200-173967200	Weak transcription	Brain Anterior Caudate	brain
38	chr1:173962200-173967200	Weak transcription	Brain Substantia Nigra	brain
39	chr1:173962200-173967200	Weak transcription	Fetal Lung	lung
40	chr1:173962200-173967400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:173962200-173967400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:173962200-173967400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:173962200-173968000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:173962200-173968600	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:173962200-173969600	Weak transcription	Brain Angular Gyrus	brain
46	chr1:173962200-173969600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:173962200-173970200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:173962200-173970400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:173962200-173970400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:173962200-173970400	Weak transcription	Ovary	ovary

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