Variant report

Variant	rs1813705
Chromosome Location	chr1:212967871-212967872
allele	A/C
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	chr1:212967628-212968381	GM12878	blood:	n/a	n/a
2	PML	chr1:212967829-212968192	GM12878	blood:	n/a	n/a
3	SPI1	chr1:212967847-212968344	K562	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
4	YY1	chr1:212967775-212968367	GM12878	blood:	n/a	n/a
5	ZNF384	chr1:212967772-212968210	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:212967766-212968323	GM12891	blood:	n/a	n/a
7	YY1	chr1:212967724-212968113	GM12892	blood:	n/a	n/a
8	TEAD4	chr1:212967820-212968318	K562	blood:	n/a	n/a
9	SP1	chr1:212967787-212968239	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:212967715-212968436	GM12891	blood:	n/a	n/a
11	SPI1	chr1:212967863-212968414	HL-60	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
12	POLR2A	chr1:212967649-212968422	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:212967863-212968267	GM12892	blood:	n/a	n/a
14	ATF2	chr1:212967693-212968426	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:212967784-212968182	GM12878	blood:	n/a	n/a
16	RUNX3	chr1:212967779-212968475	GM12878	blood:	n/a	n/a
17	TCF3	chr1:212967726-212968191	GM12878	blood:	n/a	n/a
18	SPI1	chr1:212967718-212968414	GM12891	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
19	SPI1	chr1:212967831-212968341	GM12878	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
20	POLR2A	chr1:212967767-212968324	GM12878	blood:	n/a	n/a
21	FOXM1	chr1:212967613-212968306	GM12878	blood:	n/a	n/a
22	NFIC	chr1:212967688-212968344	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:212967742-212968216	GM12878	blood:	n/a	n/a
24	STAT5A	chr1:212967690-212968323	GM12878	blood:	n/a	n/a
25	ELF1	chr1:212967766-212968390	GM12878	blood:	n/a	chr1:212968279-212968290
26	TCF12	chr1:212967789-212968178	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:212967692-212968357	Raji	blood:	n/a	n/a
28	MTA3	chr1:212967711-212968568	GM12878	blood:	n/a	n/a
29	YY1	chr1:212967784-212968168	GM12891	blood:	n/a	n/a
30	POLR2A	chr1:212967792-212968303	GM12892	blood:	n/a	n/a
31	TAF1	chr1:212967810-212968146	GM12878	blood:	n/a	n/a
32	CEBPB	chr1:212967719-212968423	GM12878	blood:	n/a	n/a
33	SPI1	chr1:212967439-212968554	GM12878	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
34	POLR2A	chr1:212967819-212968273	GM12891	blood:	n/a	n/a
35	PML	chr1:212967625-212968413	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:212967857-212968269	GM12891	blood:	n/a	n/a
37	SPI1	chr1:212967756-212968402	GM12878	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
38	CBX3	chr1:212967823-212968386	K562	blood:	n/a	n/a
39	ATF2	chr1:212967769-212968251	GM12878	blood:	n/a	n/a
40	SPI1	chr1:212967784-212968403	GM12891	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
41	SPI1	chr1:212967739-212968536	HL-60	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
42	NR2F2	chr1:212966334-212968092	K562	blood:	n/a	n/a
43	PAX5	chr1:212967797-212968247	GM12891	blood:	n/a	n/a
44	NFATC1	chr1:212967644-212968333	GM12878	blood:	n/a	n/a
45	TCF12	chr1:212967798-212968194	GM12878	blood:	n/a	n/a
46	BCLAF1	chr1:212967672-212968435	GM12878	blood:	n/a	chr1:212968281-212968290
47	POLR2A	chr1:212967827-212968372	HL-60	blood:	n/a	n/a
48	EP300	chr1:212967828-212968349	GM12878	blood:	n/a	chr1:212968273-212968283 chr1:212968280-212968289 chr1:212968279-212968293
49	POLR2A	chr1:212967756-212968377	GM12891	blood:	n/a	n/a
50	TAF1	chr1:212967769-212968202	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212965461..212968054-chr1:213031452..213034127,2	MCF-7	breast:
2	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
3	chr1:212965435..212968040-chr1:213139784..213142502,2	K562	blood:
4	chr1:212779632..212786722-chr1:212963640..212968604,10	K562	blood:
5	chr1:212779632..212786722-chr1:212965265..212968763,9	K562	blood:

Variant related genes	Relation type
TATDN3	TF binding region
NSL1	TF binding region
ENSG00000143494	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10127613	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1021994	0.84[ASN][1000 genomes]
rs1032962	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1032963	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1032964	0.93[EUR][1000 genomes]
rs1032965	0.88[ASN][1000 genomes]
rs10779583	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863992	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10864002	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120005	0.86[EUR][1000 genomes]
rs11120028	0.99[ASN][1000 genomes]
rs11120034	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120038	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12038225	0.88[ASN][1000 genomes]
rs12124669	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12133194	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12239017	0.83[EUR][1000 genomes]
rs12568552	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12744555	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12757944	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507359	0.93[EUR][1000 genomes]
rs15702	0.93[EUR][1000 genomes]
rs1580991	0.85[EUR][1000 genomes]
rs1580992	0.85[EUR][1000 genomes]
rs1605420	0.82[EUR][1000 genomes]
rs1848243	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2292214	0.91[EUR][1000 genomes]
rs2456818	0.89[ASN][1000 genomes]
rs2456827	0.93[ASN][1000 genomes]
rs2456828	0.85[ASN][1000 genomes]
rs2884675	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3738800	0.99[ASN][1000 genomes]
rs3738802	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3949369	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4639827	0.93[EUR][1000 genomes]
rs4951464	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4951639	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540766	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540767	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6665489	0.85[EUR][1000 genomes]
rs6670373	0.85[EUR][1000 genomes]
rs6670869	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6678961	0.85[EUR][1000 genomes]
rs6681851	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685864	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686145	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686164	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6689799	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6694887	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6696870	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6696908	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6700465	0.93[EUR][1000 genomes]
rs6702544	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6703982	0.85[EUR][1000 genomes]
rs7513199	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513210	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513734	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7513772	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7514070	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7522100	0.93[EUR][1000 genomes]
rs7528303	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7535608	0.93[EUR][1000 genomes]
rs7538853	0.93[EUR][1000 genomes]
rs7543603	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7547100	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555930	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1813705	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs1813705	FLVCR1-AS1	cis	Whole Blood	GTEx
rs1813705	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs1813705	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs1813705	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs1813705	FLVCR1-AS1	cis	lung	GTEx
rs1813705	NSL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212971000	Weak transcription	Small Intestine	intestine
2	chr1:212965800-212972000	Weak transcription	Gastric	stomach
3	chr1:212965800-212992600	Weak transcription	Lung	lung
4	chr1:212966000-212968200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr1:212966000-212968400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:212966000-212968400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:212966000-212970200	Weak transcription	Pancreas	Pancrea
8	chr1:212966000-212972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:212966000-212974800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
11	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
13	chr1:212966200-212968000	Enhancers	Fetal Intestine Large	intestine
14	chr1:212966200-212968400	Enhancers	Primary T cells from cord blood	blood
15	chr1:212966200-212968400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:212966200-212969000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:212966200-212970000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:212966200-212971000	Weak transcription	HSMMtube	muscle
19	chr1:212966200-212971800	Weak transcription	Fetal Kidney	kidney
20	chr1:212966200-212972000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:212966200-212973800	Weak transcription	Colonic Mucosa	Colon
22	chr1:212966200-212975600	Weak transcription	HMEC	breast
23	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:212966400-212968000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:212966400-212968000	Enhancers	Brain Angular Gyrus	brain
26	chr1:212966400-212968000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:212966400-212968200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:212966400-212968600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:212966400-212968600	Enhancers	HUVEC	blood vessel
30	chr1:212966400-212969000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:212966400-212969000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:212966400-212969000	Weak transcription	Liver	Liver
33	chr1:212966400-212969600	Enhancers	HepG2	liver
34	chr1:212966400-212970000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:212966400-212970000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:212966400-212970000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:212966400-212970000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:212966400-212970000	Weak transcription	Ovary	ovary
39	chr1:212966400-212970200	Weak transcription	Left Ventricle	heart
40	chr1:212966400-212970200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:212966400-212970400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:212966400-212970400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:212966400-212970400	Weak transcription	NH-A	brain
44	chr1:212966400-212972000	Weak transcription	Fetal Brain Female	brain
45	chr1:212966400-212972000	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:212966400-212972000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:212966400-212972000	Weak transcription	Thymus	Thymus
48	chr1:212966400-212977400	Weak transcription	Hela-S3	cervix
49	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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