Variant report

Variant	rs6786423
Chromosome Location	chr3:158450178-158450179
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	chr3:158449553-158450806	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr3:158450125-158450280	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:158449747-158450300	HUVEC	blood vessel:	n/a	n/a
4	E2F6	chr3:158449150-158450961	H1-hESC	embryonic stem cell:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
5	GTF2F1	chr3:158449566-158450180	Hela-S3	cervix:	n/a	n/a
6	MAX	chr3:158449465-158450931	A549	lung:	n/a	chr3:158449551-158449560
7	RAD21	chr3:158449698-158450183	A549	lung:	n/a	n/a
8	CHD1	chr3:158450045-158450221	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr3:158449462-158450902	Hela-S3	cervix:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
10	ZNF143	chr3:158449774-158450186	H1-hESC	embryonic stem cell:	n/a	n/a
11	RFX5	chr3:158449565-158450713	Hela-S3	cervix:	n/a	n/a
12	MAX	chr3:158449639-158450457	A549	lung:	n/a	n/a
13	CEBPB	chr3:158449669-158450932	Hela-S3	cervix:	n/a	n/a
14	HA-E2F1	chr3:158449673-158450554	Hela-S3	cervix:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
15	TCF7L2	chr3:158449320-158450575	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:158449654-158450275	HUVEC	blood vessel:	n/a	n/a
17	ELF1	chr3:158449615-158450289	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:158449725-158450339	A549	lung:	n/a	n/a
19	E2F6	chr3:158449465-158450823	A549	lung:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
20	CHD2	chr3:158449479-158450848	Hela-S3	cervix:	n/a	n/a
21	MAX	chr3:158449653-158450944	H1-hESC	embryonic stem cell:	n/a	n/a
22	SIN3A	chr3:158449403-158450925	H1-hESC	embryonic stem cell:	n/a	n/a
23	E2F6	chr3:158449637-158450249	A549	lung:	n/a	chr3:158449768-158449778
24	BACH1	chr3:158449772-158450885	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr3:158449524-158450747	Hela-S3	cervix:	n/a	chr3:158449551-158449560
26	GABPA	chr3:158449639-158450288	A549	lung:	n/a	n/a
27	E2F1	chr3:158449687-158450376	Hela-S3	cervix:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158449768-158449778
28	TAF1	chr3:158449781-158450215	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAZ	chr3:158449671-158450610	Hela-S3	cervix:	n/a	n/a
30	MXI1	chr3:158449197-158450673	IMR90	lung:	n/a	n/a
31	JUND	chr3:158449873-158450279	H1-hESC	embryonic stem cell:	n/a	n/a
32	SMARCB1	chr3:158449378-158450980	Hela-S3	cervix:	n/a	n/a
33	TCF12	chr3:158449549-158450832	A549	lung:	n/a	chr3:158449859-158449866 chr3:158449637-158449644
34	CTBP2	chr3:158449569-158450925	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr3:158449500-158450763	A549	lung:	n/a	chr3:158449551-158449560
36	ELK4	chr3:158449743-158450268	Hela-S3	cervix:	n/a	chr3:158449984-158449995
37	TBP	chr3:158449778-158450917	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:158449748-158450265	A549	lung:	n/a	n/a
39	GATA1	chr3:158449763-158451117	PBDE	blood:	n/a	n/a
40	CTCF	chr3:158450040-158450190	GM12866	blood:	n/a	n/a
41	POLR2A	chr3:158449639-158450511	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr3:158449643-158450236	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr3:158449618-158450683	Hela-S3	cervix:	n/a	n/a
44	CREB1	chr3:158449781-158450187	A549	lung:	n/a	n/a
45	POLR2A	chr3:158449667-158450584	A549	lung:	n/a	n/a
46	CEBPB	chr3:158450163-158451018	A549	lung:	n/a	n/a
47	PAX5	chr3:158449790-158450342	GM12892	blood:	n/a	n/a
48	MAX	chr3:158449347-158451065	H1-hESC	embryonic stem cell:	n/a	chr3:158449551-158449560
49	CTCF	chr3:158450140-158450290	Caco-2	colon:	n/a	n/a
50	POLR2A	chr3:158449739-158450304	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:64889401..64890183-chr3:158449447..158450182,2	Hela-S3	cervix:
2	chr3:158449938..158451943-chr3:158452978..158454973,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFM1-1	chr3:158450167-158450317	ENSG00000240207.1
2	lnc-GFM1-1	chr3:158450116-158450317	ENSG00000240207.1
3	lnc-GFM1-1	chr3:158450052-158450317	ENSG00000240207.2

Variant related genes	Relation type
ENSG00000240207	TF binding region
ENSG00000240207	Chromatin interaction
ENSG00000149792	Chromatin interaction
ENSG00000149806	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16829365	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59173444	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6441223	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6786423	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs6786423	GFM1	cis	multi-tissue	Pritchard
rs6786423	LXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449000-158450200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:158449000-158450600	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr3:158449000-158450800	Flanking Active TSS	NH-A	brain
4	chr3:158449000-158451000	Active TSS	Fetal Kidney	kidney
5	chr3:158449200-158450800	Active TSS	Brain Anterior Caudate	brain
6	chr3:158449200-158450800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr3:158449200-158451000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:158449200-158451000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr3:158449400-158450200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr3:158449400-158450400	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr3:158449400-158450400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
12	chr3:158449400-158450600	Active TSS	HSMM	muscle
13	chr3:158449400-158450600	Flanking Active TSS	HUVEC	blood vessel
14	chr3:158449400-158450800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:158449400-158450800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:158449400-158450800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:158449400-158450800	Active TSS	Small Intestine	intestine
18	chr3:158449400-158450800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
19	chr3:158449400-158451000	Active TSS	H9 Cell Line	embryonic stem cell
20	chr3:158449400-158451000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr3:158449400-158451000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:158449400-158451000	Flanking Active TSS	Right Ventricle	heart
23	chr3:158449600-158450200	Flanking Bivalent TSS/Enh	Thymus	Thymus
24	chr3:158449600-158450400	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr3:158449600-158450400	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr3:158449600-158450400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:158449600-158450400	Active TSS	Colonic Mucosa	Colon
28	chr3:158449600-158450400	Active TSS	Fetal Intestine Small	intestine
29	chr3:158449600-158450400	Active TSS	Left Ventricle	heart
30	chr3:158449600-158450600	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:158449600-158450600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:158449600-158450600	Flanking Active TSS	HMEC	breast
33	chr3:158449600-158450600	Active TSS	NHDF-Ad	bronchial
34	chr3:158449600-158450800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:158449600-158450800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr3:158449600-158450800	Active TSS	Aorta	Aorta
37	chr3:158449600-158450800	Active TSS	Psoas Muscle	Psoas
38	chr3:158449600-158451000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr3:158449600-158451000	Active TSS	Esophagus	oesophagus
40	chr3:158449600-158451000	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr3:158449600-158451600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr3:158449800-158450200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:158449800-158450200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
44	chr3:158449800-158450200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr3:158449800-158450200	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
46	chr3:158449800-158450200	Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr3:158449800-158450200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:158449800-158450200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr3:158449800-158450200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:158449800-158450200	Active TSS	Brain Germinal Matrix	brain

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