Variant report

Variant	rs2707066
Chromosome Location	chr12:122231573-122231574
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	EGR1	chr12:122231344-122231771	H1-hESC	embryonic stem cell:	n/a	chr12:122231368-122231381 chr12:122231368-122231378 chr12:122231622-122231632 chr12:122231623-122231638 chr12:122231593-122231606 chr12:122231641-122231651 chr12:122231598-122231608 chr12:122231644-122231655
2	SMC3	chr12:122231392-122233304	Hela-S3	cervix:	n/a	chr12:122232687-122232697 chr12:122233001-122233015
3	BCL3	chr12:122231462-122233359	A549	lung:	n/a	chr12:122231561-122231570 chr12:122232267-122232280
4	TFAP2C	chr12:122229602-122232569	Hela-S3	cervix:	n/a	chr12:122231521-122231536
5	GTF2F1	chr12:122231554-122231799	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:122229405-122233468	GM19099	blood:	n/a	n/a
7	ELF1	chr12:122231351-122231720	K562	blood:	n/a	chr12:122231641-122231653 chr12:122231543-122231555 chr12:122231560-122231569 chr12:122231645-122231654
8	POLR2A	chr12:122231256-122234731	H1-neurons	neurons:	n/a	n/a
9	ZKSCAN1	chr12:122231390-122232476	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:122231155-122237092	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:122231262-122233824	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:122231307-122231789	HUVEC	blood vessel:	n/a	n/a
13	EGR1	chr12:122231423-122231702	GM12878	blood:	n/a	chr12:122231622-122231632 chr12:122231623-122231638 chr12:122231593-122231606 chr12:122231641-122231651 chr12:122231598-122231608 chr12:122231644-122231655
14	TCF3	chr12:122231347-122232438	GM12878	blood:	n/a	n/a
15	SP4	chr12:122231463-122232570	H1-hESC	embryonic stem cell:	n/a	chr12:122231619-122231635 chr12:122231891-122231902 chr12:122231593-122231609
16	NRF1	chr12:122231429-122231669	GM12878	blood:	n/a	chr12:122231598-122231607 chr12:122231623-122231632
17	POLR2A	chr12:122231286-122233689	A549	lung:	n/a	n/a
18	SIN3AK20	chr12:122230934-122233186	PANC-1	pancreas:	n/a	n/a
19	MYC	chr12:122231409-122233174	A549	lung:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
20	POLR2A	chr12:122231318-122233921	HepG2	liver:	n/a	n/a
21	RAD21	chr12:122231529-122231606	H1-hESC	embryonic stem cell:	n/a	n/a
22	MTA3	chr12:122229860-122233383	GM12878	blood:	n/a	n/a
23	EP300	chr12:122231567-122232474	GM12878	blood:	n/a	chr12:122232266-122232275 chr12:122232263-122232272
24	CTCF	chr12:122231535-122233389	MCF-7	breast:	n/a	chr12:122233004-122233014 chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232999-122233017 chr12:122232322-122232335 chr12:122233001-122233022 chr12:122232312-122232325 chr12:122233002-122233015 chr12:122233000-122233016 chr12:122232299-122232308 chr12:122233002-122233011
25	POLR2A	chr12:122229522-122241538	HepG2	liver:	n/a	n/a
26	BCL3	chr12:122229500-122233523	A549	lung:	n/a	chr12:122231001-122231010 chr12:122229915-122229923 chr12:122231561-122231570 chr12:122231384-122231397 chr12:122232267-122232280 chr12:122231383-122231396
27	TCF12	chr12:122231569-122232673	ECC-1	luminal epithelium:	n/a	chr12:122231871-122231881 chr12:122232576-122232586
28	PAX5	chr12:122231388-122232654	GM12878	blood:	n/a	n/a
29	YY1	chr12:122231212-122231776	H1-hESC	embryonic stem cell:	n/a	chr12:122231560-122231569 chr12:122231376-122231387 chr12:122231645-122231654 chr12:122231598-122231607 chr12:122231563-122231577
30	CBX3	chr12:122231492-122233287	K562	blood:	n/a	n/a
31	CTCF	chr12:122231422-122233430	HCT-116	colon:	n/a	chr12:122233004-122233014 chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232999-122233017 chr12:122232322-122232335 chr12:122233001-122233022 chr12:122232312-122232325 chr12:122233002-122233015 chr12:122233000-122233016 chr12:122232299-122232308 chr12:122233002-122233011
32	TAF1	chr12:122231070-122231882	ECC-1	luminal epithelium:	n/a	n/a
33	ZNF143	chr12:122230735-122232535	GM12878	blood:	n/a	chr12:122231317-122231335 chr12:122232277-122232287 chr12:122231181-122231191 chr12:122231312-122231331
34	POLR2A	chr12:122230693-122233942	HepG2	liver:	n/a	n/a
35	CREB1	chr12:122231346-122232520	A549	lung:	n/a	n/a
36	SP4	chr12:122231542-122231855	H1-hESC	embryonic stem cell:	n/a	chr12:122231619-122231635 chr12:122231593-122231609
37	POLR2A	chr12:122231439-122231685	ProgFib	skin:	n/a	n/a
38	E2F6	chr12:122231442-122233187	A549	lung:	n/a	chr12:122231598-122231607 chr12:122231563-122231572 chr12:122231916-122231925
39	MAZ	chr12:122230686-122233217	GM12878	blood:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
40	POLR2A	chr12:122231272-122233893	GM12878	blood:	n/a	n/a
41	ZEB1	chr12:122229267-122233709	HepG2	liver:	n/a	n/a
42	POLR2A	chr12:122231247-122234639	GM12878	blood:	n/a	n/a
43	MYC	chr12:122231501-122233191	Hela-S3	cervix:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
44	EBF1	chr12:122231262-122232451	GM12878	blood:	n/a	n/a
45	CTCF	chr12:122231441-122233504	HCT-116	colon:	n/a	chr12:122233004-122233014 chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232999-122233017 chr12:122232322-122232335 chr12:122233001-122233022 chr12:122232312-122232325 chr12:122233002-122233015 chr12:122233000-122233016 chr12:122232299-122232308 chr12:122233002-122233011
46	BCLAF1	chr12:122231317-122233369	GM12878	blood:	n/a	chr12:122231561-122231570 chr12:122231384-122231397 chr12:122232267-122232280 chr12:122231383-122231396
47	MAX	chr12:122231514-122232671	H1-hESC	embryonic stem cell:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
48	POLR2A	chr12:122231351-122231909	HepG2	liver:	n/a	n/a
49	YY1	chr12:122231360-122232437	ECC-1	luminal epithelium:	n/a	chr12:122231891-122231905 chr12:122231560-122231569 chr12:122231376-122231387 chr12:122231645-122231654 chr12:122232264-122232278 chr12:122231598-122231607 chr12:122231563-122231577
50	SP1	chr12:122231327-122233297	A549	lung:	n/a	chr12:122231603-122231612 chr12:122231599-122231608 chr12:122231622-122231631 chr12:122231599-122231613 chr12:122231598-122231608 chr12:122231604-122231613 chr12:122231597-122231609 chr12:122231597-122231609 chr12:122231622-122231632 chr12:122231602-122231614 chr12:122231623-122231632 chr12:122231599-122231608 chr12:122231604-122231613 chr12:122231787-122231801 chr12:122231598-122231608 chr12:122231602-122231614 chr12:122231891-122231902 chr12:122231905-122231926 chr12:122232436-122232446 chr12:122231598-122231607 chr12:122231622-122231632 chr12:122231366-122231380 chr12:122231621-122231633 chr12:122231621-122231633

No.	Distal block	Cell Line	Cell type
1	chr12:122231121..122231717-chr7:44836710..44837609,2	Hela-S3	cervix:
2	chr12:122213783..122214655-chr12:122231473..122233403,7	MCF-7	breast:
3	chr12:122230934..122233822-chr12:122459500..122463009,3	MCF-7	breast:
4	chr12:122015890..122017624-chr12:122230329..122231836,2	MCF-7	breast:
5	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
6	chr12:122214138..122216054-chr12:122231373..122233377,2	K562	blood:
7	chr12:122213296..122215371-chr12:122231546..122233202,23	MCF-7	breast:
8	chr12:122149249..122152147-chr12:122229581..122233327,7	MCF-7	breast:
9	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
10	chr12:116997056..116999076-chr12:122230249..122232872,2	K562	blood:
11	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
12	chr12:122188669..122193873-chr12:122227176..122233304,8	MCF-7	breast:
13	chr12:122230934..122231621-chr19:39926580..39927261,2	Hela-S3	cervix:
14	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
15	chr12:120727170..120730056-chr12:122229573..122231675,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272849	TF binding region
RHOF	TF binding region
ENSG00000256950	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000196262	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000171471	Chromatin interaction
ENSG00000110801	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1004390	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11043202	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11043203	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11043207	0.82[EUR][1000 genomes]
rs1168663	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168664	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1168665	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168666	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1168668	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168669	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168671	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1168672	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168673	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12307227	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1667578	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1667579	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1795965	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1795966	0.88[AMR][1000 genomes]
rs2019561	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2019562	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2122266	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2707067	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs712852	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7957564	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7974348	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs895951	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs895952	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs895953	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs895954	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs895957	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs921286	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs921287	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs930665	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription 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 miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2707066	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122211800-122231600	Weak transcription	Brain Substantia Nigra	brain
2	chr12:122225800-122233200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr12:122227200-122231600	Weak transcription	K562	blood
4	chr12:122227400-122232000	Active TSS	Rectal Smooth Muscle	rectum
5	chr12:122228600-122232400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:122229200-122232200	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr12:122229400-122232000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:122229400-122232200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr12:122229400-122232400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:122229400-122233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:122229400-122233000	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr12:122229600-122235400	Enhancers	Fetal Heart	heart
13	chr12:122229800-122233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:122230000-122231800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:122230000-122233200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr12:122230200-122231600	Weak transcription	HSMMtube	muscle
17	chr12:122230200-122231800	Active TSS	Esophagus	oesophagus
18	chr12:122230200-122232200	Flanking Active TSS	Placenta	Placenta
19	chr12:122230200-122233000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr12:122230200-122233000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr12:122230400-122231600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:122230400-122231800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:122230400-122231800	Active TSS	Brain Cingulate Gyrus	brain
24	chr12:122230400-122231800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr12:122230400-122232000	Active TSS	Left Ventricle	heart
26	chr12:122230400-122232000	Active TSS	Small Intestine	intestine
27	chr12:122230400-122232000	Flanking Active TSS	Stomach Mucosa	stomach
28	chr12:122230400-122232400	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr12:122230400-122232800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:122230600-122231600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr12:122230600-122231800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:122230600-122231800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:122230600-122231800	Active TSS	Brain Anterior Caudate	brain
34	chr12:122230600-122231800	Active TSS	Lung	lung
35	chr12:122230600-122231800	Active TSS	Right Atrium	heart
36	chr12:122230600-122232000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:122230600-122232000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
38	chr12:122230600-122232000	Active TSS	Gastric	stomach
39	chr12:122230600-122232200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:122230600-122232200	Active TSS	Fetal Brain Female	brain
41	chr12:122230600-122232400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:122230600-122232400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr12:122230600-122232400	Active TSS	Primary T cells from cord blood	blood
44	chr12:122230600-122232400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:122230600-122232400	Active TSS	Hela-S3	cervix
46	chr12:122230600-122232600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:122230600-122232800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr12:122230600-122233000	Active TSS	H9 Cell Line	embryonic stem cell
49	chr12:122230600-122233200	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr12:122230600-122233400	Flanking Active TSS	Dnd41	blood

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