Variant report

Variant	rs41303970
Chromosome Location	chr1:94375309-94375310
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	MAFK	chr1:94374872-94375711	Hela-S3	cervix:	n/a	chr1:94375010-94375025
2	RCOR1	chr1:94374841-94375743	K562	blood:	n/a	n/a
3	POLR2A	chr1:94374596-94375426	HCT-116	colon:	n/a	n/a
4	STAT1	chr1:94374809-94375452	K562	blood:	n/a	chr1:94374912-94374924 chr1:94374998-94375007 chr1:94374997-94375006
5	ELF1	chr1:94374771-94375457	GM12878	blood:	n/a	chr1:94374838-94374850 chr1:94375073-94375085 chr1:94375131-94375143 chr1:94374903-94374912 chr1:94374954-94374966
6	CTCF	chr1:94375180-94375330	SAEC	small airway:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
7	ATF2	chr1:94375039-94375433	GM12878	blood:	n/a	n/a
8	MYC	chr1:94374780-94375542	A549	lung:	n/a	n/a
9	FOXM1	chr1:94374874-94375453	GM12878	blood:	n/a	n/a
10	CTCF	chr1:94375200-94375350	GM12865	blood:	n/a	chr1:94375220-94375236 chr1:94375221-94375234 chr1:94375225-94375234 chr1:94375219-94375237
11	CTCF	chr1:94375220-94375370	K562	blood:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234
12	TCF12	chr1:94374180-94375503	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr1:94375180-94375330	AG10803	skin:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
14	NRF1	chr1:94375006-94375616	GM12878	blood:	n/a	chr1:94375441-94375452 chr1:94375441-94375450 chr1:94375438-94375452
15	ZBTB7A	chr1:94375072-94375732	ECC-1	luminal epithelium:	n/a	chr1:94375447-94375456
16	SETDB1	chr1:94375145-94375776	U2OS	brain:	n/a	chr1:94375442-94375451
17	EP300	chr1:94374710-94375326	A549	lung:	n/a	chr1:94374842-94374858 chr1:94374840-94374849
18	TEAD4	chr1:94374885-94375501	K562	blood:	n/a	n/a
19	CTCF	chr1:94374966-94375446	K562	blood:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
20	POLR2A	chr1:94374230-94375393	GM19193	blood:	n/a	n/a
21	CTCF	chr1:94375200-94375350	HEEpiC	esophagus:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
22	CREB1	chr1:94374955-94375582	H1-hESC	embryonic stem cell:	n/a	n/a
23	TEAD4	chr1:94374935-94375445	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:94374259-94375446	GM15510	blood:	n/a	n/a
25	E2F6	chr1:94374281-94375453	K562	blood:	n/a	chr1:94375442-94375451 chr1:94374910-94374917 chr1:94374840-94374850 chr1:94374904-94374914 chr1:94374910-94374917 chr1:94374906-94374918 chr1:94375188-94375197 chr1:94374910-94374917
26	POLR2A	chr1:94374770-94375315	Hela-S3	cervix:	n/a	n/a
27	ZNF143	chr1:94374997-94375732	K562	blood:	n/a	n/a
28	ZNF384	chr1:94374829-94375635	K562	blood:	n/a	n/a
29	TBL1XR1	chr1:94374850-94375754	K562	blood:	n/a	n/a
30	MAFK	chr1:94374500-94375466	HepG2	liver:	n/a	chr1:94375010-94375025
31	HCFC1	chr1:94373924-94375533	Hela-S3	cervix:	n/a	n/a
32	ATF3	chr1:94374938-94375358	K562	blood:	n/a	chr1:94375165-94375174 chr1:94375190-94375199
33	POLR2A	chr1:94374422-94375429	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr1:94374209-94375467	GM18951	blood:	n/a	n/a
35	JUND	chr1:94374879-94375313	HepG2	liver:	n/a	n/a
36	CTCF	chr1:94375160-94375310	GM12870	blood:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
37	CTCF	chr1:94375012-94376038	K562	blood:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
38	MAFK	chr1:94374605-94375686	H1-hESC	embryonic stem cell:	n/a	chr1:94375010-94375025
39	UBTF	chr1:94374161-94375618	K562	blood:	n/a	n/a
40	CTCF	chr1:94375160-94375310	AG04450	lung:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
41	BCL3	chr1:94374857-94375401	GM12878	blood:	n/a	chr1:94375184-94375197 chr1:94374989-94374997 chr1:94375068-94375081 chr1:94374904-94374913 chr1:94374931-94374944 chr1:94374954-94374967 chr1:94375129-94375142 chr1:94374899-94374912
42	RELA	chr1:94375006-94375492	GM18951	blood:	n/a	n/a
43	POLR2A	chr1:94374730-94375359	HUVEC	blood vessel:	n/a	n/a
44	CTCF	chr1:94374978-94375564	HepG2	liver:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
45	REST	chr1:94374778-94375356	HL-60	blood:	n/a	chr1:94375197-94375210 chr1:94375324-94375337
46	CREB1	chr1:94374847-94375535	K562	blood:	n/a	n/a
47	CTCF	chr1:94375085-94375446	Spleen_OC	spleen:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237
48	JUN	chr1:94373742-94375901	K562	blood:	n/a	chr1:94374760-94374769
49	MAX	chr1:94374765-94375500	A549	lung:	n/a	n/a
50	CTCF	chr1:94375200-94375350	SK-N-SH_RA	brain:	n/a	chr1:94375221-94375234 chr1:94375220-94375236 chr1:94375225-94375234 chr1:94375219-94375237

No.	Distal block	Cell Line	Cell type
1	chr1:94337226..94339966-chr1:94373816..94376815,2	K562	blood:
2	chr1:94372270..94376088-chr1:94480112..94484516,4	K562	blood:
3	chr1:94312303..94314752-chr1:94373572..94376301,2	MCF-7	breast:
4	chr1:94375220..94377246-chr1:94405325..94407050,2	MCF-7	breast:
5	chr1:94343199..94347658-chr1:94372955..94376562,9	MCF-7	breast:
6	chr1:94344690..94346304-chr1:94373768..94376372,3	MCF-7	breast:
7	chr1:93811453..93813762-chr1:94372603..94376116,3	K562	blood:
8	chr1:94310847..94313357-chr1:94374431..94376609,2	K562	blood:
9	chr1:94342014..94348814-chr1:94369991..94376733,14	K562	blood:

Variant related genes	Relation type
GCLM	TF binding region
ENSG00000260464	Chromatin interaction
ENSG00000117505	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000223745	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000198691	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10159000	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10489607	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874811	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874812	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165031	0.94[ASN][1000 genomes]
rs11165034	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165037	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12068168	0.85[ASN][1000 genomes]
rs12068345	0.95[ASN][1000 genomes]
rs12089163	0.94[ASN][1000 genomes]
rs12122406	0.91[ASN][1000 genomes]
rs12129986	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130623	0.92[ASN][1000 genomes]
rs12131163	0.91[ASN][1000 genomes]
rs12131247	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12135991	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140097	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12401354	0.87[ASN][1000 genomes]
rs1473711	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1989020	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1989021	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017736	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2092697	0.91[ASN][1000 genomes]
rs2143993	0.91[ASN][1000 genomes]
rs2273406	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2391324	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35674584	0.92[ASN][1000 genomes]
rs3827715	0.97[ASN][1000 genomes]
rs4573532	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4598495	0.94[ASN][1000 genomes]
rs57387172	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60120441	0.94[ASN][1000 genomes]
rs61667071	0.94[ASN][1000 genomes]
rs6680027	0.93[ASN][1000 genomes]
rs6681078	0.94[ASN][1000 genomes]
rs6696758	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6699912	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700112	0.94[ASN][1000 genomes]
rs718873	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718874	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718875	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743119	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7536714	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761889	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769211	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523355	chr1:94351328-94385591	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3404764	chr1:94372564-94377162	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3426478	chr1:94373589-94376737	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41303970	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94369600-94375800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:94372400-94375800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:94372400-94375800	Active TSS	NHLF	lung
4	chr1:94372800-94376000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:94373200-94375600	Active TSS	Brain Angular Gyrus	brain
6	chr1:94373200-94375800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:94373400-94375800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:94373400-94375800	Active TSS	HSMMtube	muscle
9	chr1:94373600-94375400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:94373600-94375400	Active TSS	K562	blood
11	chr1:94373600-94375600	Active TSS	Psoas Muscle	Psoas
12	chr1:94373600-94375600	Active TSS	A549	lung
13	chr1:94373600-94375600	Active TSS	HepG2	liver
14	chr1:94373600-94375800	Active TSS	NHDF-Ad	bronchial
15	chr1:94373800-94375400	Active TSS	Placenta	Placenta
16	chr1:94373800-94375600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:94373800-94375600	Active TSS	Right Atrium	heart
18	chr1:94373800-94375600	Active TSS	Thymus	Thymus
19	chr1:94373800-94375600	Active TSS	HSMM	muscle
20	chr1:94373800-94375800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr1:94373800-94375800	Active TSS	Colonic Mucosa	Colon
22	chr1:94373800-94375800	Active TSS	HUVEC	blood vessel
23	chr1:94373800-94375800	Active TSS	NH-A	brain
24	chr1:94374000-94375400	Active TSS	Primary T cells fromperipheralblood	blood
25	chr1:94374000-94375400	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr1:94374000-94375400	Active TSS	Small Intestine	intestine
27	chr1:94374000-94375600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:94374000-94375600	Active TSS	Fetal Intestine Large	intestine
29	chr1:94374000-94375600	Active TSS	Ovary	ovary
30	chr1:94374000-94375600	Active TSS	Right Ventricle	heart
31	chr1:94374000-94375800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:94374000-94375800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:94374000-94375800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:94374000-94375800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:94374000-94375800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:94374000-94375800	Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:94374000-94375800	Active TSS	Aorta	Aorta
38	chr1:94374000-94375800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:94374000-94375800	Active TSS	Fetal Muscle Trunk	muscle
40	chr1:94374000-94375800	Active TSS	NHEK	skin
41	chr1:94374000-94375800	Active TSS	Osteobl	bone
42	chr1:94374000-94376000	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr1:94374200-94375400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr1:94374200-94375400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:94374200-94375400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:94374200-94375400	Active TSS	Gastric	stomach
47	chr1:94374200-94375400	Active TSS	Spleen	Spleen
48	chr1:94374200-94375400	Active TSS	Hela-S3	cervix
49	chr1:94374200-94375600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:94374200-94375600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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