Variant report

Variant	rs6441224
Chromosome Location	chr3:158450417-158450418
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	MYC	chr3:158450342-158450760	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:158449553-158450806	Hela-S3	cervix:	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	MAX	chr3:158449465-158450931	A549	lung:	n/a	chr3:158449551-158449560
5	CEBPB	chr3:158450397-158450822	IMR90	lung:	n/a	n/a
6	GABPA	chr3:158450185-158450529	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr3:158449462-158450902	Hela-S3	cervix:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
8	POLR2A	chr3:158450358-158450618	A549	lung:	n/a	n/a
9	RFX5	chr3:158449565-158450713	Hela-S3	cervix:	n/a	n/a
10	MAX	chr3:158449639-158450457	A549	lung:	n/a	n/a
11	CEBPB	chr3:158449669-158450932	Hela-S3	cervix:	n/a	n/a
12	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
13	CTCF	chr3:158450373-158450433	GM13977	blood:	n/a	n/a
14	TCF7L2	chr3:158449320-158450575	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:158450400-158450798	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F6	chr3:158449465-158450823	A549	lung:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
17	CEBPB	chr3:158450401-158450805	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD2	chr3:158449479-158450848	Hela-S3	cervix:	n/a	n/a
19	MAX	chr3:158449653-158450944	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIN3A	chr3:158449403-158450925	H1-hESC	embryonic stem cell:	n/a	n/a
21	CEBPB	chr3:158450372-158450827	MCF-7	breast:	n/a	n/a
22	BACH1	chr3:158449772-158450885	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:158450294-158450757	Hela-S3	cervix:	n/a	n/a
24	MAX	chr3:158449524-158450747	Hela-S3	cervix:	n/a	chr3:158449551-158449560
25	MAZ	chr3:158449671-158450610	Hela-S3	cervix:	n/a	n/a
26	MXI1	chr3:158449197-158450673	IMR90	lung:	n/a	n/a
27	ZKSCAN1	chr3:158450408-158450621	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:158450341-158450570	A549	lung:	n/a	n/a
29	SMARCB1	chr3:158449378-158450980	Hela-S3	cervix:	n/a	n/a
30	TCF12	chr3:158449549-158450832	A549	lung:	n/a	chr3:158449859-158449866 chr3:158449637-158449644
31	CTBP2	chr3:158449569-158450925	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr3:158449500-158450763	A549	lung:	n/a	chr3:158449551-158449560
33	TBP	chr3:158449778-158450917	H1-hESC	embryonic stem cell:	n/a	n/a
34	GATA1	chr3:158449763-158451117	PBDE	blood:	n/a	n/a
35	POLR2A	chr3:158449639-158450511	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr3:158450317-158450581	A549	lung:	n/a	n/a
37	POLR2A	chr3:158449618-158450683	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:158449667-158450584	A549	lung:	n/a	n/a
39	CEBPB	chr3:158450163-158451018	A549	lung:	n/a	n/a
40	MAX	chr3:158449347-158451065	H1-hESC	embryonic stem cell:	n/a	chr3:158449551-158449560
41	CEBPB	chr3:158450320-158450808	A549	lung:	n/a	n/a
42	CEBPB	chr3:158450295-158450797	A549	lung:	n/a	n/a
43	POLR2A	chr3:158449712-158450652	H1-hESC	embryonic stem cell:	n/a	n/a
44	HMGN3	chr3:158450408-158450514	K562	blood:	n/a	n/a
45	POLR2A	chr3:158449252-158450772	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr3:158450200-158450581	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158449938..158451943-chr3:158452978..158454973,2	K562	blood:

Variant related genes	Relation type
RARRES1	TF binding region
ENSG00000240207	TF binding region
ENSG00000240207	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1006911	0.91[ASN][1000 genomes]
rs1346834	0.91[ASN][1000 genomes]
rs17699456	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1864508	0.91[ASN][1000 genomes]
rs2115941	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2364927	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2566346	0.89[ASN][1000 genomes]
rs2615052	0.89[ASN][1000 genomes]
rs4680460	0.89[ASN][1000 genomes]
rs4680467	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs57932243	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61794797	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441225	0.91[ASN][1000 genomes]
rs6783879	0.85[ASN][1000 genomes]
rs6802315	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6804249	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7615751	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7618110	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7635993	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9822005	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9825696	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9840571	0.86[ASN][1000 genomes]
rs9861938	0.98[ASN][1000 genomes]
rs9863103	0.98[ASN][1000 genomes]
rs9866134	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9881462	0.91[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6441224	RARRES1	cis	cerebellar cortex	BrainEAC
rs6441224	RARRES1	cis	brain	BrainEAC
rs6441224	RARRES1	cis	frontal cortex	BrainEAC
rs6441224	RARRES1	cis	thalamus	BrainEAC
rs6441224	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs6441224	MLF1	cis	Heart Left Ventricle	GTEx
rs6441224	RARRES1	cis	occipital cortex	BrainEAC

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449000-158450600	Active TSS	Sigmoid Colon	Sigmoid Colon
2	chr3:158449000-158450800	Flanking Active TSS	NH-A	brain
3	chr3:158449000-158451000	Active TSS	Fetal Kidney	kidney
4	chr3:158449200-158450800	Active TSS	Brain Anterior Caudate	brain
5	chr3:158449200-158450800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr3:158449200-158451000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:158449200-158451000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:158449400-158450600	Active TSS	HSMM	muscle
9	chr3:158449400-158450600	Flanking Active TSS	HUVEC	blood vessel
10	chr3:158449400-158450800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:158449400-158450800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:158449400-158450800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:158449400-158450800	Active TSS	Small Intestine	intestine
14	chr3:158449400-158450800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr3:158449400-158451000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:158449400-158451000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr3:158449400-158451000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:158449400-158451000	Flanking Active TSS	Right Ventricle	heart
19	chr3:158449600-158450600	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:158449600-158450600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:158449600-158450600	Flanking Active TSS	HMEC	breast
22	chr3:158449600-158450600	Active TSS	NHDF-Ad	bronchial
23	chr3:158449600-158450800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:158449600-158450800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr3:158449600-158450800	Active TSS	Aorta	Aorta
26	chr3:158449600-158450800	Active TSS	Psoas Muscle	Psoas
27	chr3:158449600-158451000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr3:158449600-158451000	Active TSS	Esophagus	oesophagus
29	chr3:158449600-158451000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr3:158449600-158451600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:158449800-158450600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:158449800-158450600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:158449800-158450600	Active TSS	Primary T cells from cord blood	blood
34	chr3:158449800-158450600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr3:158449800-158450600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:158449800-158450600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:158449800-158450600	Active TSS	Liver	Liver
38	chr3:158449800-158450600	Bivalent/Poised TSS	Fetal Brain Female	brain
39	chr3:158449800-158450600	Active TSS	Fetal Intestine Large	intestine
40	chr3:158449800-158450600	Active TSS	Gastric	stomach
41	chr3:158449800-158450600	Active TSS	Stomach Mucosa	stomach
42	chr3:158449800-158450800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr3:158449800-158450800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:158449800-158450800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:158449800-158450800	Active TSS	Brain Angular Gyrus	brain
46	chr3:158449800-158450800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr3:158449800-158450800	Active TSS	Brain Substantia Nigra	brain
48	chr3:158449800-158450800	Active TSS	Fetal Lung	lung
49	chr3:158449800-158450800	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr3:158449800-158450800	Active TSS	Rectal Smooth Muscle	rectum

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