Variant report

Variant	rs231238
Chromosome Location	chr19:36248666-36248667
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	SIN3A	chr19:36248582-36249584	GM12878	blood:	n/a	chr19:36249080-36249091
2	GABPA	chr19:36248654-36249372	MCF-7	breast:	n/a	chr19:36249057-36249066
3	POLR2A	chr19:36247961-36249593	MCF10A-Er-Src	breast:	n/a	n/a
4	SP2	chr19:36248538-36249204	HepG2	liver:	n/a	chr19:36248970-36248980 chr19:36248843-36248866 chr19:36248908-36248931
5	POLR2A	chr19:36248252-36248686	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr19:36247523-36249660	U87	brain:	n/a	n/a
7	ELK1	chr19:36248364-36249455	Hela-S3	cervix:	n/a	n/a
8	E2F4	chr19:36248438-36249590	MCF10A-Er-Src	breast:	n/a	chr19:36248628-36248637 chr19:36248674-36248683
9	SP1	chr19:36248145-36249680	HCT-116	colon:	n/a	chr19:36249017-36249029 chr19:36249018-36249028 chr19:36249014-36249028 chr19:36249456-36249468 chr19:36248961-36248982 chr19:36249019-36249028 chr19:36249018-36249027 chr19:36249017-36249029 chr19:36249017-36249028 chr19:36249019-36249028 chr19:36249018-36249028
10	NANOG	chr19:36248540-36249195	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr19:36248359-36249270	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOSL2	chr19:36248666-36249417	A549	lung:	n/a	chr19:36248678-36248687 chr19:36248679-36248688 chr19:36248839-36248848
13	POLR2A	chr19:36247429-36249863	PANC-1	pancreas:	n/a	n/a
14	TCF12	chr19:36247866-36249803	SK-N-SH	brain:	n/a	chr19:36248579-36248589
15	POLR2A	chr19:36247887-36249617	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr19:36248651-36248949	HepG2	liver:	n/a	n/a
17	HDAC2	chr19:36248284-36248680	K562	blood:	n/a	n/a
18	FOS	chr19:36248426-36249150	K562	blood:	n/a	chr19:36248678-36248687 chr19:36248679-36248688 chr19:36248839-36248848
19	CHD2	chr19:36248660-36249621	K562	blood:	n/a	n/a
20	EP300	chr19:36247984-36249247	SK-N-SH	brain:	n/a	n/a
21	REST	chr19:36248257-36248692	SK-N-SH	brain:	n/a	chr19:36248543-36248556
22	GABPA	chr19:36248587-36249682	SK-N-SH	brain:	n/a	chr19:36249057-36249066
23	POLR2A	chr19:36247565-36249515	PFSK-1	brain:	n/a	n/a
24	FOXM1	chr19:36248548-36249741	GM12878	blood:	n/a	chr19:36249489-36249497
25	POLR2A	chr19:36243424-36249712	IMR90	lung:	n/a	n/a
26	MAZ	chr19:36248207-36249541	Hela-S3	cervix:	n/a	n/a
27	NFIC	chr19:36248613-36249069	GM12878	blood:	n/a	chr19:36248895-36248923
28	SIX5	chr19:36247941-36249863	A549	lung:	n/a	chr19:36249248-36249257 chr19:36249246-36249255 chr19:36249244-36249258
29	CREB1	chr19:36248248-36249659	A549	lung:	n/a	n/a
30	ZBTB33	chr19:36248654-36249677	SK-N-SH	brain:	n/a	chr19:36249058-36249068
31	POLR2A	chr19:36248182-36249565	PBDE	blood:	n/a	n/a
32	CEBPB	chr19:36248411-36248743	H1-hESC	embryonic stem cell:	n/a	n/a
33	BRCA1	chr19:36248662-36249630	Hela-S3	cervix:	n/a	chr19:36248709-36248716
34	MAX	chr19:36248141-36249747	A549	lung:	n/a	n/a
35	POLR2A	chr19:36247962-36249523	HCT-116	colon:	n/a	n/a
36	TCF12	chr19:36248049-36248822	SK-N-SH	brain:	n/a	chr19:36248579-36248589
37	POLR2A	chr19:36248177-36249491	HepG2	liver:	n/a	n/a
38	TAF1	chr19:36248622-36249357	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr19:36248158-36249560	K562	blood:	n/a	n/a
40	POLR2A	chr19:36248223-36249503	H1-hESC	embryonic stem cell:	n/a	n/a
41	PBX3	chr19:36247547-36249734	A549	lung:	n/a	chr19:36248844-36248864 chr19:36248627-36248636
42	POLR2A	chr19:36247499-36249815	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr19:36248620-36248904	SK-N-SH	brain:	n/a	n/a
44	RUNX3	chr19:36248403-36249681	GM12878	blood:	n/a	chr19:36248813-36248822
45	USF2	chr19:36248548-36249025	Hela-S3	cervix:	n/a	n/a
46	MAX	chr19:36248441-36249556	A549	lung:	n/a	n/a
47	ATF3	chr19:36248653-36249536	A549	lung:	n/a	chr19:36248689-36248697 chr19:36249002-36249011
48	NFYA	chr19:36248624-36249300	GM12878	blood:	n/a	chr19:36248628-36248640 chr19:36248969-36248983
49	POLR2A	chr19:36248605-36249467	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr19:36248615-36248910	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64037188..64037741-chr19:36248285..36249182,2	NB4	blood:
2	chr19:36247404..36252021-chr19:36265348..36272678,7	MCF-7	breast:
3	chr19:36248580..36254743-chr19:36274692..36280659,6	K562	blood:
4	chr19:36206099..36210841-chr19:36246614..36251827,8	MCF-7	breast:
5	chr19:36245255..36250047-chr19:36263979..36267864,8	K562	blood:
6	chr19:36231491..36233720-chr19:36248400..36250494,2	MCF-7	breast:
7	chr19:36238866..36244880-chr19:36246037..36252437,21	MCF-7	breast:
8	chr19:36247959..36249985-chr19:36390079..36391606,2	MCF-7	breast:
9	chr19:36247584..36253409-chr19:36264102..36268750,7	K562	blood:

Variant related genes	Relation type
HSPB6	TF binding region
C19orf55	TF binding region
ENSG00000267439	TF binding region
ENSG00000267796	Chromatin interaction
ENSG00000126246	Chromatin interaction
ENSG00000267439	Chromatin interaction
ENSG00000167604	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000004777	Chromatin interaction
ENSG00000173264	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs107068	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1269214	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs173003	0.82[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs179570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242522	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242523	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2285421	0.85[CEU][hapmap]
rs231244	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs231588	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs231591	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs231592	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55939240	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs614225	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs807478	0.88[EUR][1000 genomes]
rs807479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs807485	0.81[GIH][hapmap]
rs9917056	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs231238	CCDC97	cis	cerebellum	SCAN
rs231238	COX6B1	cis	Muscle Skeletal	GTEx
rs231238	FBXO27	cis	parietal	SCAN
rs231238	COX6B1	trans	parietal	SCAN
rs231238	AC002398.13	cis	Thyroid	GTEx
rs231238	SAMD4B	cis	parietal	SCAN
rs231238	COX6B1	cis	Heart Left Ventricle	GTEx
rs231238	LYPD4	cis	cerebellum	SCAN
rs231238	ZBTB32	cis	Nerve Tibial	GTEx
rs231238	ZNF568	cis	cerebellum	SCAN
rs231238	PHLDB3	cis	cerebellum	SCAN
rs231238	ZBTB32	cis	Thyroid	GTEx
rs231238	COX6B1	trans	cerebellum	SCAN
rs231238	CEACAM3	cis	cerebellum	SCAN
rs231238	MEGF8	cis	parietal	SCAN
rs231238	RN7SL765P	cis	Muscle Skeletal	GTEx
rs231238	ZNF780B	cis	cerebellum	SCAN
rs231238	UPK1A	trans	cerebellum	SCAN
rs231238	ZBTB32	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36246000-36248800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:36246000-36248800	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr19:36246000-36248800	Flanking Active TSS	Fetal Muscle Trunk	muscle
4	chr19:36246000-36249800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:36246200-36248800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:36246200-36248800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:36246200-36249400	Active TSS	Aorta	Aorta
8	chr19:36246200-36250000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:36246400-36248800	Flanking Active TSS	Fetal Muscle Leg	muscle
10	chr19:36246400-36249800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:36246400-36249800	Active TSS	Rectal Smooth Muscle	rectum
12	chr19:36246400-36250000	Active TSS	Psoas Muscle	Psoas
13	chr19:36246400-36250200	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr19:36246800-36248800	Flanking Active TSS	Placenta	Placenta
15	chr19:36246800-36248800	Flanking Active TSS	NH-A	brain
16	chr19:36247000-36248800	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr19:36247200-36249600	Active TSS	Ovary	ovary
18	chr19:36247200-36250000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr19:36247400-36248800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr19:36247400-36249800	Active TSS	Fetal Kidney	kidney
21	chr19:36247600-36248800	Enhancers	Gastric	stomach
22	chr19:36247600-36248800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr19:36247800-36248800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr19:36247800-36250000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr19:36248000-36248800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr19:36248000-36248800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr19:36248000-36248800	Flanking Active TSS	Fetal Stomach	stomach
28	chr19:36248000-36249800	Active TSS	Right Atrium	heart
29	chr19:36248200-36249600	Active TSS	Colon Smooth Muscle	Colon
30	chr19:36248200-36249800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:36248200-36249800	Active TSS	Right Ventricle	heart
32	chr19:36248200-36250200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:36248400-36248800	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr19:36248400-36248800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:36248400-36248800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:36248400-36248800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:36248400-36248800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:36248400-36248800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:36248400-36248800	Flanking Active TSS	Liver	Liver
40	chr19:36248400-36248800	Enhancers	Fetal Heart	heart
41	chr19:36248400-36248800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr19:36248400-36249400	Active TSS	Brain Angular Gyrus	brain
43	chr19:36248400-36249400	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr19:36248400-36249400	Active TSS	Small Intestine	intestine
45	chr19:36248400-36249600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:36248400-36249600	Active TSS	HSMMtube	muscle
47	chr19:36248400-36249800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr19:36248400-36249800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:36248400-36249800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:36248400-36249800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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