Variant report

Variant	rs877129
Chromosome Location	chr12:32909240-32909241
allele	A/C
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	SP1	chr12:32907966-32909540	A549	lung:	n/a	chr12:32908853-32908863 chr12:32908853-32908863
2	MAFK	chr12:32908916-32909480	H1-hESC	embryonic stem cell:	n/a	n/a
3	RCOR1	chr12:32907898-32909492	K562	blood:	n/a	n/a
4	CTCF	chr12:32909068-32909541	T-47D	breast:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
5	TBL1XR1	chr12:32908691-32909509	K562	blood:	n/a	n/a
6	POLR2A	chr12:32907993-32909311	HCT-116	colon:	n/a	n/a
7	TCF12	chr12:32907811-32909714	A549	lung:	n/a	chr12:32909534-32909541
8	BCLAF1	chr12:32907948-32909537	GM12878	blood:	n/a	chr12:32908870-32908878 chr12:32909348-32909357 chr12:32908001-32908010
9	TEAD4	chr12:32908455-32909463	HepG2	liver:	n/a	n/a
10	USF1	chr12:32908672-32909481	A549	lung:	n/a	n/a
11	CTCF	chr12:32909200-32909350	GM12870	blood:	n/a	chr12:32909331-32909344 chr12:32909328-32909346
12	POLR2A	chr12:32907855-32909357	Hela-S3	cervix:	n/a	n/a
13	TCF12	chr12:32908585-32909336	A549	lung:	n/a	n/a
14	TBP	chr12:32907948-32909463	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:32907953-32909446	K562	blood:	n/a	n/a
16	MYC	chr12:32906916-32909509	NB4	blood:	n/a	n/a
17	POLR2A	chr12:32907874-32909611	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr12:32907735-32909605	HUVEC	blood vessel:	n/a	n/a
19	CTCF	chr12:32909166-32909474	HUVEC	blood vessel:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
20	NRF1	chr12:32908719-32909269	Hela-S3	cervix:	n/a	chr12:32908903-32908914 chr12:32908900-32908914 chr12:32908903-32908914
21	JUND	chr12:32907875-32909494	K562	blood:	n/a	chr12:32909451-32909458
22	CTCF	chr12:32909140-32909717	H1-hESC	embryonic stem cell:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
23	POU2F2	chr12:32908012-32909543	GM12878	blood:	n/a	chr12:32909123-32909145
24	CEBPB	chr12:32908491-32909579	GM12878	blood:	n/a	chr12:32909343-32909360 chr12:32909207-32909220
25	RELA	chr12:32908040-32909437	GM19099	blood:	n/a	n/a
26	CBX3	chr12:32908620-32909509	K562	blood:	n/a	n/a
27	RAD21	chr12:32908797-32909517	A549	lung:	n/a	chr12:32909329-32909348
28	CTCF	chr12:32909171-32909482	GM12878	blood:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
29	RAD21	chr12:32909041-32909544	H1-hESC	embryonic stem cell:	n/a	chr12:32909329-32909348
30	RAD21	chr12:32909198-32909417	K562	blood:	n/a	chr12:32909329-32909348
31	CTCF	chr12:32909240-32909390	K562	blood:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
32	RAD21	chr12:32908819-32909764	A549	lung:	n/a	chr12:32909329-32909348
33	MAX	chr12:32907929-32909452	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr12:32907961-32909288	GM12878	blood:	n/a	n/a
35	CTCF	chr12:32909220-32909370	A549	lung:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
36	POLR2A	chr12:32907773-32909513	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr12:32907909-32909371	HCT-116	colon:	n/a	n/a
38	MBD4	chr12:32908494-32909328	HepG2	liver:	n/a	n/a
39	POLR2A	chr12:32908491-32909539	U87	brain:	n/a	n/a
40	CTCF	chr12:32909107-32909569	A549	lung:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
41	CTCF	chr12:32909240-32909390	HL-60	blood:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
42	CTCF	chr12:32909129-32909639	MCF-7	breast:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
43	CTCF	chr12:32907827-32909638	HCT-116	colon:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
44	CTCF	chr12:32909191-32909427	Fibrobl	skin:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
45	RAD21	chr12:32909129-32909588	HepG2	liver:	n/a	chr12:32909329-32909348
46	CHD1	chr12:32908617-32909420	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr12:32909220-32909370	GM12878	blood:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
48	POLR2A	chr12:32907123-32909529	MCF10A-Er-Src	breast:	n/a	n/a
49	BHLHE40	chr12:32908012-32909513	K562	blood:	n/a	n/a
50	CTCF	chr12:32909200-32909350	HMEC	breast:	n/a	chr12:32909331-32909344 chr12:32909328-32909346

No.	Distal block	Cell Line	Cell type
1	chr12:32907107..32909879-chr12:32974270..32975942,2	K562	blood:
2	chr12:32830720..32834017-chr12:32907137..32909476,4	K562	blood:
3	chr12:32909198..32910124-chr12:33071777..33072639,3	MCF-7	breast:
4	chr12:32908997..32909668-chr12:33099946..33100757,2	MCF-7	breast:
5	chr12:32908900..32910812-chr12:32911585..32914530,2	K562	blood:
6	chr12:32908793..32909708-chr16:28834212..28834892,2	NB4	blood:
7	chr12:32908939..32909783-chr12:33758798..33759372,2	MCF-7	breast:
8	chr12:32908990..32910670-chr12:34173573..34175511,2	K562	blood:
9	chr12:32832004..32833946-chr12:32906988..32909887,3	MCF-7	breast:
10	chr12:32908405..32909605-chr12:34174701..34175708,3	MCF-7	breast:
11	chr12:32908860..32909807-chr12:33048872..33049669,2	MCF-7	breast:
12	chr12:32908961..32909825-chr12:33071724..33072321,3	MCF-7	breast:
13	chr12:32902299..32904984-chr12:32908343..32910409,2	K562	blood:
14	chr12:32902284..32904491-chr12:32907257..32909806,2	K562	blood:
15	chr12:32908157..32910268-chr12:33048253..33050625,4	MCF-7	breast:

Variant related genes	Relation type
YARS2	TF binding region
ENSG00000139131	Chromatin interaction
ENSG00000168488	Chromatin interaction
ENSG00000087470	Chromatin interaction
ENSG00000139133	Chromatin interaction
ENSG00000057294	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10506096	1.00[AMR][1000 genomes]
rs16920084	1.00[AMR][1000 genomes]
rs16920116	1.00[AMR][1000 genomes]
rs16920125	0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs55653318	1.00[AMR][1000 genomes]
rs55961287	1.00[AMR][1000 genomes]
rs56160613	1.00[AMR][1000 genomes]
rs56231715	1.00[AMR][1000 genomes]
rs56671444	1.00[AMR][1000 genomes]
rs57389939	1.00[AMR][1000 genomes]
rs57842976	1.00[AMR][1000 genomes]
rs58682304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59670367	1.00[AMR][1000 genomes]
rs60243898	1.00[AMR][1000 genomes]
rs60330503	1.00[AMR][1000 genomes]
rs60697901	0.98[AFR][1000 genomes]
rs74072674	1.00[AMR][1000 genomes]
rs74072685	1.00[AMR][1000 genomes]
rs74072936	1.00[AMR][1000 genomes]
rs74072944	1.00[AMR][1000 genomes]
rs74072945	1.00[AMR][1000 genomes]
rs74073029	1.00[AMR][1000 genomes]
rs74073061	1.00[AMR][1000 genomes]
rs74073064	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74073069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1051667	chr12:32871860-32919673	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1042661	chr12:32871860-32928833	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1050779	chr12:32872999-32921973	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv532334	chr12:32884789-33034791	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs877129	NAAA	trans	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32906800-32909400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:32906800-32909400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:32906800-32909800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:32907000-32909400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr12:32907000-32909400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:32907000-32909400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:32907000-32909400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:32907000-32909400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:32907000-32909400	Active TSS	Fetal Intestine Large	intestine
10	chr12:32907000-32909400	Active TSS	Psoas Muscle	Psoas
11	chr12:32907200-32909400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:32907200-32909400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr12:32907200-32909400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:32907400-32909400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:32907400-32909400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:32907400-32909400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr12:32907400-32909400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr12:32907400-32909400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr12:32907400-32909400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr12:32907400-32909400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:32907400-32909400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr12:32907400-32909400	Active TSS	K562	blood
23	chr12:32907600-32909400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr12:32907600-32909400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:32907600-32909400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr12:32907600-32909400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:32907600-32909400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:32907600-32909400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:32907600-32909400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:32907600-32909400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:32907600-32909400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr12:32907600-32909400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:32907600-32909400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:32907600-32909400	Active TSS	Fetal Intestine Small	intestine
35	chr12:32907600-32909400	Active TSS	Fetal Kidney	kidney
36	chr12:32907600-32909400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr12:32907600-32909400	Active TSS	Left Ventricle	heart
38	chr12:32907600-32909400	Active TSS	Ovary	ovary
39	chr12:32907600-32909400	Active TSS	Rectal Smooth Muscle	rectum
40	chr12:32907600-32909400	Active TSS	Small Intestine	intestine
41	chr12:32907600-32909400	Active TSS	A549	lung
42	chr12:32907600-32909400	Active TSS	HSMM	muscle
43	chr12:32907600-32909400	Active TSS	HSMMtube	muscle
44	chr12:32907600-32909400	Active TSS	NHLF	lung
45	chr12:32907600-32909600	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr12:32907800-32909400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:32907800-32909400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:32907800-32909400	Active TSS	Esophagus	oesophagus
49	chr12:32907800-32909400	Active TSS	Pancreas	Pancrea
50	chr12:32908000-32909400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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