Variant report

Variant	rs6441223
Chromosome Location	chr3:158449965-158449966
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	POLR2A	chr3:158449553-158450806	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:158449747-158450300	HUVEC	blood vessel:	n/a	n/a
3	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
4	CTCF	chr3:158449900-158450050	GM12865	blood:	n/a	n/a
5	GTF2F1	chr3:158449566-158450180	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr3:158449900-158450050	HVMF	connective:	n/a	n/a
7	MAX	chr3:158449465-158450931	A549	lung:	n/a	chr3:158449551-158449560
8	CTCF	chr3:158449920-158450070	HUVEC	blood vessel:	n/a	n/a
9	TCF3	chr3:158449672-158449995	GM12878	blood:	n/a	n/a
10	CTCF	chr3:158449920-158450070	AG09319	gingival:	n/a	n/a
11	POLR2A	chr3:158449933-158450062	MCF10A-Er-Src	breast:	n/a	n/a
12	RAD21	chr3:158449849-158450149	IMR90	lung:	n/a	n/a
13	CTCF	chr3:158449940-158450090	GM12869	blood:	n/a	n/a
14	CTCF	chr3:158449962-158450062	ProgFib	skin:	n/a	n/a
15	CTCF	chr3:158449940-158450090	HA-sp	spinal cord:	n/a	n/a
16	RAD21	chr3:158449698-158450183	A549	lung:	n/a	n/a
17	RAD21	chr3:158449871-158450075	SK-N-SH_RA	brain:	n/a	n/a
18	TEAD4	chr3:158449695-158449966	H1-hESC	embryonic stem cell:	n/a	n/a
19	ELK1	chr3:158449820-158450153	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:158449806-158450068	A549	lung:	n/a	n/a
21	MYC	chr3:158449850-158450014	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr3:158449744-158450059	GM12878	blood:	n/a	n/a
23	E2F6	chr3:158449462-158450902	Hela-S3	cervix:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
24	ZNF143	chr3:158449774-158450186	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr3:158449864-158450055	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr3:158449942-158450048	Pancreas_OC	pancreas:	n/a	n/a
27	CTCF	chr3:158449960-158450110	GM12874	blood:	n/a	n/a
28	CTCF	chr3:158449960-158450110	SK-N-SH_RA	brain:	n/a	n/a
29	RFX5	chr3:158449565-158450713	Hela-S3	cervix:	n/a	n/a
30	MAX	chr3:158449639-158450457	A549	lung:	n/a	n/a
31	CEBPB	chr3:158449669-158450932	Hela-S3	cervix:	n/a	n/a
32	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
33	CTCF	chr3:158449960-158450110	HCM	heart:	n/a	n/a
34	CTCF	chr3:158449940-158450090	AG04450	lung:	n/a	n/a
35	TCF7L2	chr3:158449320-158450575	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr3:158449869-158450109	Fibrobl	skin:	n/a	n/a
37	CTCF	chr3:158449940-158450090	AG09309	skin:	n/a	n/a
38	POLR2A	chr3:158449654-158450275	HUVEC	blood vessel:	n/a	n/a
39	ELF1	chr3:158449615-158450289	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:158449725-158450339	A549	lung:	n/a	n/a
41	E2F6	chr3:158449465-158450823	A549	lung:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
42	RAD21	chr3:158449857-158450095	SK-N-SH_RA	brain:	n/a	n/a
43	CTCF	chr3:158449880-158450030	Hela-S3	cervix:	n/a	n/a
44	CHD2	chr3:158449479-158450848	Hela-S3	cervix:	n/a	n/a
45	MAX	chr3:158449653-158450944	H1-hESC	embryonic stem cell:	n/a	n/a
46	SIN3A	chr3:158449403-158450925	H1-hESC	embryonic stem cell:	n/a	n/a
47	GTF2F1	chr3:158449892-158450029	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF7L2	chr3:158449825-158450045	PANC-1	pancreas:	n/a	n/a
49	CTCF	chr3:158449920-158450070	HVMF	connective:	n/a	n/a
50	CTCF	chr3:158449936-158450081	GM19238	blood:	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:

Variant related genes	Relation type
MFSD1	TF binding region
ENSG00000240207	TF binding region
ENSG00000240207	Chromatin interaction
ENSG00000149806	Chromatin interaction
ENSG00000149792	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	0.80[ASN][1000 genomes]
rs59173444	0.80[ASN][1000 genomes]
rs6786423	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
rs6441223	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs6441223	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs6441223	GFM1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449000-158450000	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr3:158449000-158450200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:158449000-158450600	Active TSS	Sigmoid Colon	Sigmoid Colon
4	chr3:158449000-158450800	Flanking Active TSS	NH-A	brain
5	chr3:158449000-158451000	Active TSS	Fetal Kidney	kidney
6	chr3:158449200-158450000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:158449200-158450000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:158449200-158450000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr3:158449200-158450000	Flanking Active TSS	Osteobl	bone
10	chr3:158449200-158450800	Active TSS	Brain Anterior Caudate	brain
11	chr3:158449200-158450800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:158449200-158451000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr3:158449200-158451000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:158449400-158450000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:158449400-158450000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:158449400-158450000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:158449400-158450000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:158449400-158450000	Flanking Active TSS	Pancreas	Pancrea
19	chr3:158449400-158450000	Enhancers	Spleen	Spleen
20	chr3:158449400-158450200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:158449400-158450400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr3:158449400-158450400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
23	chr3:158449400-158450600	Active TSS	HSMM	muscle
24	chr3:158449400-158450600	Flanking Active TSS	HUVEC	blood vessel
25	chr3:158449400-158450800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:158449400-158450800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:158449400-158450800	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr3:158449400-158450800	Active TSS	Small Intestine	intestine
29	chr3:158449400-158450800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr3:158449400-158451000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr3:158449400-158451000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr3:158449400-158451000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:158449400-158451000	Flanking Active TSS	Right Ventricle	heart
34	chr3:158449600-158450200	Flanking Bivalent TSS/Enh	Thymus	Thymus
35	chr3:158449600-158450400	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr3:158449600-158450400	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr3:158449600-158450400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:158449600-158450400	Active TSS	Colonic Mucosa	Colon
39	chr3:158449600-158450400	Active TSS	Fetal Intestine Small	intestine
40	chr3:158449600-158450400	Active TSS	Left Ventricle	heart
41	chr3:158449600-158450600	Enhancers	Primary B cells from peripheral blood	blood
42	chr3:158449600-158450600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:158449600-158450600	Flanking Active TSS	HMEC	breast
44	chr3:158449600-158450600	Active TSS	NHDF-Ad	bronchial
45	chr3:158449600-158450800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:158449600-158450800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr3:158449600-158450800	Active TSS	Aorta	Aorta
48	chr3:158449600-158450800	Active TSS	Psoas Muscle	Psoas
49	chr3:158449600-158451000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr3:158449600-158451000	Active TSS	Esophagus	oesophagus

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