Variant report

Variant	rs1075728
Chromosome Location	chr19:42462788-42462789
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	JUND	chr19:42461862-42463043	A549	lung:	n/a	chr19:42462612-42462621
2	POLR2A	chr19:42462780-42463870	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:42462700-42463860	K562	blood:	n/a	n/a
4	CHD2	chr19:42462755-42462955	GM12878	blood:	n/a	n/a
5	YY1	chr19:42462747-42464167	SK-N-SH	brain:	n/a	chr19:42463633-42463643 chr19:42464100-42464111 chr19:42464065-42464084
6	POLR2A	chr19:42462708-42463064	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr19:42462674-42463092	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr19:42462612-42463657	MCF-7	breast:	n/a	n/a
9	POLR2A	chr19:42462737-42463046	GM12878	blood:	n/a	n/a
10	ZKSCAN1	chr19:42462705-42462985	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr19:42462411-42463812	A549	lung:	n/a	n/a
12	POLR2A	chr19:42462683-42463048	K562	blood:	n/a	n/a
13	POLR2A	chr19:42462717-42463786	GM19193	blood:	n/a	n/a
14	RCOR1	chr19:42462738-42463024	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:42462667-42463881	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr19:42462731-42463049	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:42462587-42463071	HCT-116	colon:	n/a	n/a
18	BCL3	chr19:42461632-42463085	A549	lung:	n/a	chr19:42461923-42461932 chr19:42462605-42462618
19	HEY1	chr19:42462722-42463127	K562	blood:	n/a	n/a
20	MAX	chr19:42461926-42462827	Hela-S3	cervix:	n/a	chr19:42462647-42462658
21	POLR2A	chr19:42462461-42463868	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr19:42462549-42463646	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:42462684-42463711	Gliobla	brain:	n/a	n/a
24	TAF1	chr19:42462594-42463808	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr19:42461665-42464274	A549	lung:	n/a	chr19:42463323-42463333 chr19:42462647-42462658
26	POLR2A	chr19:42462716-42463128	A549	lung:	n/a	n/a
27	HEY1	chr19:42462668-42463115	HepG2	liver:	n/a	n/a
28	RUNX3	chr19:42461841-42462860	GM12878	blood:	n/a	chr19:42462358-42462373
29	POLR2A	chr19:42462727-42463071	HepG2	liver:	n/a	n/a
30	POLR2A	chr19:42462734-42463658	HepG2	liver:	n/a	n/a
31	MAZ	chr19:42461698-42464029	IMR90	lung:	n/a	chr19:42463323-42463333 chr19:42462647-42462658
32	POLR2A	chr19:42462471-42464185	H1-hESC	embryonic stem cell:	n/a	n/a
33	SP1	chr19:42462337-42463004	GM12878	blood:	n/a	chr19:42462808-42462819 chr19:42462829-42462840
34	POLR2A	chr19:42462754-42463045	HepG2	liver:	n/a	n/a
35	POLR2A	chr19:42462552-42463889	U87	brain:	n/a	n/a
36	MAZ	chr19:42462502-42463002	HepG2	liver:	n/a	chr19:42462647-42462658
37	MYC	chr19:42462757-42463975	K562	blood:	n/a	chr19:42463323-42463333
38	HEY1	chr19:42462760-42463029	HepG2	liver:	n/a	n/a
39	SIN3AK20	chr19:42461282-42464072	A549	lung:	n/a	n/a
40	BCL3	chr19:42461508-42464170	A549	lung:	n/a	chr19:42461923-42461932 chr19:42462605-42462618
41	POLR2A	chr19:42462722-42463162	GM12891	blood:	n/a	n/a
42	CTCF	chr19:42462720-42462870	HCPEpiC	choroid plexus:	n/a	n/a
43	CCNT2	chr19:42462524-42463822	K562	blood:	n/a	chr19:42463106-42463115 chr19:42463329-42463338 chr19:42462693-42462702
44	CTCF	chr19:42461471-42462896	HCT-116	colon:	n/a	chr19:42462088-42462098 chr19:42462607-42462620 chr19:42461914-42461923 chr19:42462085-42462103 chr19:42462607-42462620
45	POLR2A	chr19:42462499-42463810	GM12892	blood:	n/a	n/a
46	E2F6	chr19:42462000-42463242	A549	lung:	n/a	chr19:42462487-42462495
47	CREB1	chr19:42461946-42464046	HepG2	liver:	n/a	n/a
48	CTCF	chr19:42461186-42464240	A549	lung:	n/a	chr19:42464107-42464120 chr19:42462088-42462098 chr19:42462607-42462620 chr19:42461914-42461923 chr19:42462085-42462103 chr19:42462607-42462620
49	REST	chr19:42462517-42464159	H1-neurons	neurons:	n/a	chr19:42463829-42463838 chr19:42463103-42463116 chr19:42463820-42463833
50	POLR2A	chr19:42462747-42463080	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42362135..42368129-chr19:42461941..42464761,7	MCF-7	breast:
2	chr19:42430426..42435985-chr19:42461209..42463660,4	K562	blood:
3	chr19:42379146..42381960-chr19:42461841..42465419,3	MCF-7	breast:
4	chr19:42361051..42365836-chr19:42460461..42465209,10	K562	blood:
5	chr19:42362252..42368846-chr19:42460307..42464966,15	MCF-7	breast:
6	chr19:42461278..42463492-chr20:55838965..55841655,2	MCF-7	breast:
7	chr19:42361938..42366462-chr19:42459916..42465209,13	K562	blood:
8	chr19:42363659..42364430-chr19:42462556..42463157,2	K562	blood:
9	chr19:42387951..42392334-chr19:42459610..42463737,7	MCF-7	breast:
10	chr19:42460531..42463518-chr19:42578179..42580939,2	K562	blood:
11	chr19:42460466..42464604-chr19:42577075..42581382,5	MCF-7	breast:
12	chr19:42385735..42391033-chr19:42460351..42463651,6	K562	blood:
13	chr19:42385036..42390018-chr19:42460408..42463391,5	K562	blood:
14	chr19:42462261..42465397-chr19:42579731..42582911,4	MCF-7	breast:
15	chr19:42462621..42465324-chr19:42490447..42493373,2	MCF-7	breast:
16	chr19:42385318..42391505-chr19:42458040..42463569,9	MCF-7	breast:

Variant related genes	Relation type
RABAC1	TF binding region
ENSG00000076928	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000105409	Chromatin interaction
ENSG00000105369	Chromatin interaction
ENSG00000105372	Chromatin interaction
ENSG00000105732	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs12977527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35287851	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs891167	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1075728	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs1075728	EHD2	cis	parietal	SCAN
rs1075728	SLC1A5	cis	parietal	SCAN
rs1075728	ZNF227	cis	cerebellum	SCAN
rs1075728	LIG1	cis	parietal	SCAN
rs1075728	TMEM143	cis	parietal	SCAN
rs1075728	SNORD32A	cis	parietal	SCAN
rs1075728	RABAC1	cis	Whole Blood	GTEx
rs1075728	PVR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42461200-42462800	Flanking Active TSS	Duodenum Mucosa	Duodenum
2	chr19:42461600-42462800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:42461600-42462800	Flanking Active TSS	A549	lung
4	chr19:42461800-42462800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr19:42461800-42462800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:42461800-42462800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr19:42461800-42462800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:42461800-42462800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:42461800-42462800	Flanking Active TSS	Brain Substantia Nigra	brain
10	chr19:42461800-42462800	Enhancers	Fetal Brain Male	brain
11	chr19:42461800-42462800	Flanking Active TSS	HepG2	liver
12	chr19:42461800-42462800	Flanking Active TSS	HUVEC	blood vessel
13	chr19:42461800-42462800	Flanking Active TSS	NH-A	brain
14	chr19:42461800-42462800	Flanking Active TSS	NHLF	lung
15	chr19:42461800-42464000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr19:42462000-42462800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:42462000-42462800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:42462000-42462800	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr19:42462000-42462800	Flanking Active TSS	Fetal Heart	heart
20	chr19:42462000-42462800	Flanking Active TSS	NHDF-Ad	bronchial
21	chr19:42462000-42462800	Flanking Active TSS	Osteobl	bone
22	chr19:42462000-42463000	Flanking Active TSS	Fetal Brain Female	brain
23	chr19:42462000-42463000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr19:42462000-42463000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr19:42462000-42463200	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr19:42462000-42463200	Flanking Active TSS	Dnd41	blood
27	chr19:42462000-42463400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:42462000-42464000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr19:42462200-42462800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
30	chr19:42462200-42462800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:42462200-42462800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:42462200-42462800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:42462200-42462800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr19:42462200-42462800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr19:42462200-42462800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:42462200-42462800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:42462200-42462800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr19:42462200-42462800	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr19:42462200-42462800	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr19:42462200-42462800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr19:42462200-42462800	Flanking Active TSS	Colonic Mucosa	Colon
42	chr19:42462200-42462800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr19:42462200-42462800	Flanking Active TSS	Fetal Intestine Small	intestine
44	chr19:42462200-42462800	Flanking Active TSS	Fetal Lung	lung
45	chr19:42462200-42462800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr19:42462200-42462800	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr19:42462200-42462800	Flanking Active TSS	GM12878-XiMat	blood
48	chr19:42462200-42462800	Flanking Active TSS	HMEC	breast
49	chr19:42462200-42463000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:42462200-42463000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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