Variant report

Variant	rs56247945
Chromosome Location	chr1:173910964-173910965
allele	A/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	POLR2A	chr1:173910824-173911131	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173808363..173810424-chr1:173909776..173912123,2	MCF-7	breast:
2	chr1:173833863..173839457-chr1:173910408..173918981,14	MCF-7	breast:

Variant related genes	Relation type
RC3H1	TF binding region
ENSG00000208317	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10798302	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10912719	0.93[ASN][1000 genomes]
rs10912722	0.89[ASN][1000 genomes]
rs12063313	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12066153	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076799	0.87[ASN][1000 genomes]
rs12092774	0.89[ASN][1000 genomes]
rs12096785	0.89[ASN][1000 genomes]
rs12097809	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12563395	0.80[ASN][1000 genomes]
rs13375086	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884994	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951627	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61547493	0.83[ASN][1000 genomes]
rs61826843	0.80[ASN][1000 genomes]
rs61826844	0.80[ASN][1000 genomes]
rs6665484	0.93[ASN][1000 genomes]
rs6673632	0.90[ASN][1000 genomes]
rs6677660	0.88[ASN][1000 genomes]
rs6686083	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689285	0.89[ASN][1000 genomes]
rs6696163	0.87[ASN][1000 genomes]
rs714624	0.89[ASN][1000 genomes]
rs7413166	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511780	0.80[ASN][1000 genomes]
rs7514069	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538312	0.89[ASN][1000 genomes]
rs7547280	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554915	0.89[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	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
3	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv3407396	chr1:173896346-173917122	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56247945	SERPINC1	cis	lung	GTEx
rs56247945	SERPINC1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:173894600-173914400	Weak transcription	Right Ventricle	heart
3	chr1:173895200-173912200	Weak transcription	Stomach Mucosa	stomach
4	chr1:173896400-173914400	Weak transcription	Pancreas	Pancrea
5	chr1:173898000-173915200	Weak transcription	Aorta	Aorta
6	chr1:173898200-173912200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:173898800-173912200	Weak transcription	NHEK	skin
8	chr1:173899200-173913800	Weak transcription	Fetal Heart	heart
9	chr1:173899400-173917400	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:173899400-173927200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:173899400-173929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:173899600-173923200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:173899800-173953800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:173900000-173911000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:173900000-173929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:173900000-173958600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:173900200-173912400	Weak transcription	Fetal Brain Male	brain
21	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:173901200-173931400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:173901600-173912800	Strong transcription	HSMM	muscle
27	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:173901600-173966400	Strong transcription	Dnd41	blood
29	chr1:173902200-173921200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:173902200-173928200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr1:173902200-173954600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:173902600-173954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:173903200-173925000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr1:173903200-173925600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:173903400-173915600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:173903400-173917400	Strong transcription	HUVEC	blood vessel
37	chr1:173903400-173927000	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:173903400-173927000	Strong transcription	Fetal Thymus	thymus
39	chr1:173903800-173912600	Weak transcription	Brain Angular Gyrus	brain
40	chr1:173904000-173929200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:173904200-173912400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:173904800-173921400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:173904800-173921400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:173904800-173923200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:173904800-173954200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:173905000-173911000	Strong transcription	NH-A	brain
48	chr1:173905000-173927000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:173905000-173938400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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