Variant report

Variant	rs61827902
Chromosome Location	chr1:174130434-174130435
allele	C/G
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	EBF1	chr1:174130431-174130723	GM12878	blood:	n/a	n/a
2	RUNX3	chr1:174130251-174131149	GM12878	blood:	n/a	n/a
3	PAX5	chr1:174130381-174130724	GM12878	blood:	n/a	chr1:174130532-174130551
4	POLR2A	chr1:174127459-174131155	GM18505	blood:	n/a	n/a
5	POLR2A	chr1:174130293-174131271	GM12892	blood:	n/a	n/a
6	PAX5	chr1:174130382-174130771	GM12892	blood:	n/a	chr1:174130532-174130551
7	PAX5	chr1:174130411-174130688	GM12892	blood:	n/a	chr1:174130532-174130551
8	PAX5	chr1:174130346-174130686	GM12878	blood:	n/a	chr1:174130532-174130551
9	POLR2A	chr1:174130351-174130678	GM12878	blood:	n/a	n/a
10	RUNX3	chr1:174130357-174131038	GM12878	blood:	n/a	n/a
11	PAX5	chr1:174130379-174131176	GM12878	blood:	n/a	chr1:174130532-174130551
12	PAX5	chr1:174130434-174130671	GM12878	blood:	n/a	chr1:174130532-174130551
13	POLR2A	chr1:174130385-174130526	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:174130399-174130748	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:174130228-174130843	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:174129282..174131364-chr1:174167925..174169764,2	K562	blood:
2	chr1:174128312..174130705-chr1:174967510..174969928,2	K562	blood:
3	chr1:173445824..173447952-chr1:174128991..174131620,2	K562	blood:
4	chr1:173835729..173840438-chr1:174127915..174131019,7	K562	blood:

Variant related genes	Relation type
ENSG00000227373	TF binding region
ENSG00000234741	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000238872	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10127823	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10494491	0.82[EUR][1000 genomes]
rs12562344	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12562959	0.82[EUR][1000 genomes]
rs12564848	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12564858	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12564876	1.00[AFR][1000 genomes]
rs12565675	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12565973	0.82[EUR][1000 genomes]
rs12566022	0.82[EUR][1000 genomes]
rs12566642	0.82[EUR][1000 genomes]
rs12566643	0.95[EUR][1000 genomes]
rs12566842	0.82[EUR][1000 genomes]
rs12567854	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12567864	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12568869	1.00[AFR][1000 genomes]
rs12737218	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1321637	0.82[EUR][1000 genomes]
rs1407126	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16828467	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846667	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16846688	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1890881	0.95[EUR][1000 genomes]
rs2015075	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2025241	0.82[EUR][1000 genomes]
rs28595073	0.82[EUR][1000 genomes]
rs36013663	0.82[EUR][1000 genomes]
rs41265242	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs41266044	0.95[EUR][1000 genomes]
rs4140468	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56926540	0.82[EUR][1000 genomes]
rs57651489	0.87[EUR][1000 genomes]
rs58866024	0.90[EUR][1000 genomes]
rs60005461	0.90[EUR][1000 genomes]
rs60039606	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826771	0.82[EUR][1000 genomes]
rs61826777	0.81[EUR][1000 genomes]
rs61826779	0.82[EUR][1000 genomes]
rs61826780	0.81[EUR][1000 genomes]
rs61826784	0.81[EUR][1000 genomes]
rs61826824	0.82[EUR][1000 genomes]
rs61826826	0.81[EUR][1000 genomes]
rs61826829	0.84[EUR][1000 genomes]
rs61826831	0.84[EUR][1000 genomes]
rs61826863	1.00[AFR][1000 genomes]
rs61826865	1.00[AFR][1000 genomes]
rs61827889	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827900	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61828571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61828574	0.92[EUR][1000 genomes]
rs61828575	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828576	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828577	0.95[EUR][1000 genomes]
rs61828578	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828580	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828583	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828584	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828587	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828589	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828590	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828591	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828592	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828595	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828622	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61828624	0.87[EUR][1000 genomes]
rs61828625	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61828627	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61828630	1.00[AFR][1000 genomes]
rs61828631	1.00[AFR][1000 genomes]
rs61828635	1.00[AFR][1000 genomes]
rs61828645	1.00[AFR][1000 genomes]
rs61828653	1.00[AFR][1000 genomes]
rs61828895	0.82[EUR][1000 genomes]
rs61828898	0.82[EUR][1000 genomes]
rs61828899	0.82[EUR][1000 genomes]
rs6684527	0.82[EUR][1000 genomes]
rs7525325	0.94[EUR][1000 genomes]
rs9425779	0.82[EUR][1000 genomes]
rs965498	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61827902	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174128000-174131400	Active TSS	GM12878-XiMat	blood
2	chr1:174128000-174131600	Active TSS	Duodenum Mucosa	Duodenum
3	chr1:174129000-174132600	Active TSS	Right Atrium	heart
4	chr1:174129600-174131000	Weak transcription	Esophagus	oesophagus
5	chr1:174129600-174131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:174129600-174132600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:174129600-174134000	Weak transcription	Stomach Mucosa	stomach
8	chr1:174129600-174164800	Weak transcription	Gastric	stomach
9	chr1:174129600-174173200	Weak transcription	Pancreas	Pancrea
10	chr1:174129800-174130600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:174129800-174130800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:174129800-174131000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:174129800-174131000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:174129800-174131000	Weak transcription	Psoas Muscle	Psoas
15	chr1:174129800-174131200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:174129800-174131400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:174129800-174131400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:174129800-174131800	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:174129800-174131800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:174129800-174133200	Weak transcription	Small Intestine	intestine
21	chr1:174129800-174134800	Weak transcription	Ovary	ovary
22	chr1:174129800-174135000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:174129800-174135000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:174129800-174135000	Weak transcription	Spleen	Spleen
25	chr1:174129800-174137000	Weak transcription	Fetal Lung	lung
26	chr1:174129800-174145600	Weak transcription	Fetal Thymus	thymus
27	chr1:174129800-174147000	Weak transcription	Fetal Brain Male	brain
28	chr1:174129800-174149600	Weak transcription	Aorta	Aorta
29	chr1:174130000-174130800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:174130000-174130800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:174130000-174130800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:174130000-174130800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:174130000-174130800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:174130000-174131200	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:174130000-174131400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:174130000-174131400	Weak transcription	Thymus	Thymus
37	chr1:174130000-174131600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:174130000-174131800	Enhancers	Dnd41	blood
39	chr1:174130000-174132000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr1:174130000-174132000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:174130000-174133200	Weak transcription	Colonic Mucosa	Colon
42	chr1:174130000-174133200	Weak transcription	Fetal Intestine Large	intestine
43	chr1:174130000-174133200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:174130000-174133600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:174130000-174134800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:174130000-174134800	Weak transcription	Adipose Nuclei	Adipose
47	chr1:174130000-174134800	Weak transcription	Liver	Liver
48	chr1:174130000-174134800	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:174130000-174135400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:174130000-174135400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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