Variant report

Variant	rs6541075
Chromosome Location	chr1:10092770-10092771
allele	A/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	CTCF	chr1:10092614-10092829	ECC-1	luminal epithelium:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
2	CTCF	chr1:10092589-10092872	GM13977	blood:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
3	CTCF	chr1:10092348-10093080	HCT-116	colon:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
4	RAD21	chr1:10092491-10092864	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:10092490-10092792	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr1:10092447-10093952	K562	blood:	n/a	chr1:10093004-10093017 chr1:10093001-10093020 chr1:10093006-10093015 chr1:10093007-10093016 chr1:10093004-10093017 chr1:10093004-10093017 chr1:10093005-10093016 chr1:10092822-10092831 chr1:10093006-10093015
7	GTF2F1	chr1:10092459-10093961	Hela-S3	cervix:	n/a	n/a
8	YY1	chr1:10092305-10093785	SK-N-SH	brain:	n/a	chr1:10093018-10093035 chr1:10093025-10093033 chr1:10092794-10092808 chr1:10092791-10092805 chr1:10092835-10092846 chr1:10092800-10092811 chr1:10092600-10092609 chr1:10093024-10093034 chr1:10092795-10092809 chr1:10093012-10093034 chr1:10092878-10092889 chr1:10093023-10093031
9	CTCF	chr1:10092640-10092790	HCM	heart:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
10	NFIC	chr1:10092317-10093451	GM12878	blood:	n/a	n/a
11	CTCF	chr1:10092640-10092790	HPAF	blood vessel:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
12	TCF3	chr1:10092638-10092872	GM12878	blood:	n/a	n/a
13	ATF2	chr1:10092493-10092998	GM12878	blood:	n/a	n/a
14	RCOR1	chr1:10092406-10093971	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:10092703-10093586	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr1:10092442-10092912	K562	blood:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
17	CTCF	chr1:10092462-10092874	A549	lung:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
18	CTCF	chr1:10092620-10092770	GM12871	blood:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
19	RUNX3	chr1:10092497-10093036	GM12878	blood:	n/a	n/a
20	RAD21	chr1:10092499-10092895	HepG2	liver:	n/a	n/a
21	HEY1	chr1:10092466-10092829	K562	blood:	n/a	chr1:10092793-10092808
22	TCF7L2	chr1:10092493-10093885	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr1:10092245-10094157	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr1:10092640-10092790	AG04449	skin:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
25	JUND	chr1:10092462-10093704	K562	blood:	n/a	chr1:10092988-10092997
26	TAF1	chr1:10092490-10092775	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr1:10092598-10092862	GM10266	blood:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
28	POLR2A	chr1:10092506-10092836	H1-hESC	embryonic stem cell:	n/a	n/a
29	IRF1	chr1:10092415-10094093	K562	blood:	n/a	chr1:10093173-10093187 chr1:10092572-10092592 chr1:10093168-10093182 chr1:10092983-10092997 chr1:10092902-10092916 chr1:10092572-10092585 chr1:10092577-10092591
30	EP300	chr1:10092492-10093179	H1-hESC	embryonic stem cell:	n/a	chr1:10092873-10092889 chr1:10092796-10092805
31	RAD21	chr1:10092449-10093005	MCF-7	breast:	n/a	n/a
32	NR2F2	chr1:10092243-10094003	K562	blood:	n/a	n/a
33	ELF1	chr1:10092470-10093573	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:10092392-10093928	H1-neurons	neurons:	n/a	n/a
35	POLR2A	chr1:10092521-10092800	A549	lung:	n/a	n/a
36	CREB1	chr1:10092461-10093186	A549	lung:	n/a	n/a
37	CTCF	chr1:10092512-10092865	H1-hESC	embryonic stem cell:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
38	SP1	chr1:10092366-10093381	A549	lung:	n/a	chr1:10092859-10092868 chr1:10093200-10093209 chr1:10093168-10093180 chr1:10092904-10092913 chr1:10093198-10093210 chr1:10093165-10093179 chr1:10092986-10093000 chr1:10092833-10092842 chr1:10092831-10092843 chr1:10092985-10092997 chr1:10092902-10092913 chr1:10093199-10093208 chr1:10093170-10093179 chr1:10092891-10092902 chr1:10092832-10092841 chr1:10093174-10093184 chr1:10093141-10093150 chr1:10092985-10092997 chr1:10092903-10092912 chr1:10093140-10093154 chr1:10092831-10092843 chr1:10093198-10093210 chr1:10092987-10092996 chr1:10092986-10092995 chr1:10092760-10092774 chr1:10093169-10093178
39	CTCF	chr1:10092640-10092790	GM12871	blood:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
40	MAX	chr1:10092453-10094091	Hela-S3	cervix:	n/a	chr1:10093004-10093017 chr1:10093001-10093020 chr1:10093006-10093015 chr1:10093007-10093016 chr1:10093004-10093017 chr1:10093004-10093017 chr1:10093005-10093016 chr1:10092822-10092831 chr1:10093006-10093015
41	MAZ	chr1:10092270-10094033	IMR90	lung:	n/a	chr1:10093004-10093017 chr1:10093001-10093020 chr1:10093006-10093015 chr1:10093007-10093016 chr1:10093004-10093017 chr1:10093004-10093017 chr1:10093005-10093016 chr1:10092822-10092831 chr1:10093006-10093015
42	CTCF	chr1:10092640-10092790	AG10803	skin:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
43	EP300	chr1:10092540-10094968	K562	blood:	n/a	chr1:10094798-10094808 chr1:10092873-10092889 chr1:10094604-10094618 chr1:10092796-10092805
44	CTCF	chr1:10092596-10092863	H1-hESC	embryonic stem cell:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
45	MAFK	chr1:10092411-10094018	Hela-S3	cervix:	n/a	n/a
46	MAX	chr1:10092393-10093037	A549	lung:	n/a	chr1:10093004-10093017 chr1:10093001-10093020 chr1:10093006-10093015 chr1:10093007-10093016 chr1:10093004-10093017 chr1:10093004-10093017 chr1:10093005-10093016 chr1:10092822-10092831 chr1:10093006-10093015
47	BACH1	chr1:10092409-10092852	K562	blood:	n/a	n/a
48	PML	chr1:10092570-10094057	K562	blood:	n/a	n/a
49	CTCF	chr1:10092604-10092846	Medullo	brain:	n/a	chr1:10092715-10092731 chr1:10092716-10092729 chr1:10092716-10092729 chr1:10092719-10092732
50	POLR2A	chr1:10092160-10093931	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:10002061..10004916-chr1:10091716..10094596,6	MCF-7	breast:
2	chr1:10002125..10006916-chr1:10090169..10095056,10	K562	blood:
3	chr1:10002086..10005062-chr1:10091281..10093134,5	K562	blood:
4	chr1:10001502..10006445-chr1:10090966..10096976,9	MCF-7	breast:
5	chr1:10002756..10003923-chr1:10092230..10093198,5	K562	blood:
6	chr1:10092606..10093229-chr20:30194353..30195124,2	Hela-S3	cervix:
7	chr1:10002308..10002961-chr1:10092373..10092897,2	MCF-7	breast:
8	chr1:9929452..9932865-chr1:10092666..10095157,3	K562	blood:
9	chr1:9968980..9971143-chr1:10091275..10094032,2	MCF-7	breast:

Variant related genes	Relation type
UBE4B	TF binding region
ENSG00000178585	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000228150	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs3003376	0.84[EUR][1000 genomes]
rs3013788	0.84[EUR][1000 genomes]
rs3123522	0.84[EUR][1000 genomes]
rs58528460	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6676280	0.84[EUR][1000 genomes]
rs6693449	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7528979	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9919194	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[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	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6541075	LZIC	cis	multi-tissue	Pritchard
rs6541075	LZIC	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10085800-10093000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:10089600-10093000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:10090400-10093000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:10090600-10092800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:10091600-10094400	Active TSS	A549	lung
6	chr1:10091800-10093000	Weak transcription	Spleen	Spleen
7	chr1:10092200-10093000	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:10092200-10093000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:10092200-10093200	Enhancers	Fetal Brain Male	brain
10	chr1:10092200-10093400	Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr1:10092200-10093400	Active TSS	Brain Germinal Matrix	brain
12	chr1:10092200-10093600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:10092200-10094000	Active TSS	Fetal Lung	lung
14	chr1:10092200-10094200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:10092200-10094200	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:10092200-10094600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:10092200-10094600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:10092200-10094800	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:10092200-10094800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:10092200-10095600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:10092200-10096200	Active TSS	K562	blood
22	chr1:10092400-10092800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr1:10092400-10092800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:10092400-10092800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:10092400-10092800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr1:10092400-10092800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:10092400-10092800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:10092400-10092800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr1:10092400-10092800	Flanking Active TSS	Dnd41	blood
30	chr1:10092400-10092800	Flanking Active TSS	HSMM	muscle
31	chr1:10092400-10092800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr1:10092400-10092800	Flanking Active TSS	NHLF	lung
33	chr1:10092400-10093000	Enhancers	Primary hematopoietic stem cells	blood
34	chr1:10092400-10093000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:10092400-10093000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:10092400-10093200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:10092400-10093200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:10092400-10093400	Active TSS	Primary T cells from cord blood	blood
39	chr1:10092400-10093400	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:10092400-10093400	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr1:10092400-10093600	Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr1:10092400-10093600	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:10092400-10093800	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr1:10092400-10093800	Active TSS	Brain Anterior Caudate	brain
45	chr1:10092400-10093800	Active TSS	Brain Hippocampus Middle	brain
46	chr1:10092400-10094000	Active TSS	Brain Substantia Nigra	brain
47	chr1:10092400-10094000	Active TSS	Duodenum Mucosa	Duodenum
48	chr1:10092400-10094000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr1:10092400-10094000	Active TSS	Pancreas	Pancrea
50	chr1:10092400-10094000	Active TSS	Stomach Mucosa	stomach

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