Variant report

Variant	rs7979296
Chromosome Location	chr12:25348514-25348515
allele	G/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	HMGN3	chr12:25347931-25348759	K562	blood:	n/a	n/a
2	MXI1	chr12:25347216-25349605	SK-N-SH	brain:	n/a	chr12:25348081-25348096
3	POLR2A	chr12:25347861-25348663	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:25348054-25348986	K562	blood:	n/a	n/a
5	CTCF	chr12:25348420-25348570	HMF	breast:	n/a	chr12:25348515-25348524
6	POLR2A	chr12:25347504-25348981	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:25347957-25348851	H1-hESC	embryonic stem cell:	n/a	n/a
8	RCOR1	chr12:25347923-25348647	HepG2	liver:	n/a	n/a
9	FOXM1	chr12:25347744-25348767	GM12878	blood:	n/a	n/a
10	TBP	chr12:25348003-25348837	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr12:25347959-25348689	K562	blood:	n/a	chr12:25348515-25348524
12	POLR2A	chr12:25348031-25348565	GM12892	blood:	n/a	n/a
13	MYC	chr12:25348042-25348890	MCF10A-Er-Src	breast:	n/a	chr12:25348097-25348107
14	EP300	chr12:25348058-25348919	K562	blood:	n/a	chr12:25348282-25348291 chr12:25348251-25348267 chr12:25348624-25348634
15	POLR2A	chr12:25347826-25348658	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr12:25347983-25348816	HEK293	kidney:	n/a	n/a
17	RAD21	chr12:25348004-25348653	SK-N-SH_RA	brain:	n/a	n/a
18	POLR2A	chr12:25347803-25348709	HL-60	blood:	n/a	n/a
19	ELF1	chr12:25347859-25348692	GM12878	blood:	n/a	chr12:25348284-25348293
20	POLR2A	chr12:25347800-25348551	ProgFib	skin:	n/a	n/a
21	BCL3	chr12:25347759-25348635	A549	lung:	n/a	chr12:25348126-25348139
22	RUNX3	chr12:25347939-25348952	GM12878	blood:	n/a	chr12:25348502-25348511 chr12:25348502-25348511 chr12:25348240-25348257
23	MAX	chr12:25347873-25348622	GM12878	blood:	n/a	chr12:25348097-25348107
24	SIN3AK20	chr12:25347883-25348587	K562	blood:	n/a	n/a
25	ELF1	chr12:25347807-25348589	GM12878	blood:	n/a	chr12:25348284-25348293
26	ELF1	chr12:25347855-25348575	MCF-7	breast:	n/a	chr12:25348284-25348293
27	POLR2A	chr12:25348005-25348608	GM18526	blood:	n/a	n/a
28	SIN3AK20	chr12:25347853-25348595	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr12:25347992-25348540	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr12:25347927-25348520	Gliobla	brain:	n/a	n/a
31	MAX	chr12:25347800-25348746	ECC-1	luminal epithelium:	n/a	chr12:25348097-25348107
32	MAX	chr12:25347943-25348661	K562	blood:	n/a	chr12:25348097-25348107
33	TBP	chr12:25347826-25349005	K562	blood:	n/a	n/a
34	MAX	chr12:25347923-25348588	HepG2	liver:	n/a	chr12:25348097-25348107
35	HCFC1	chr12:25347139-25349028	Hela-S3	cervix:	n/a	n/a
36	EP300	chr12:25347949-25349040	GM12878	blood:	n/a	chr12:25348282-25348291 chr12:25348251-25348267 chr12:25348624-25348634
37	TAF1	chr12:25347979-25348669	A549	lung:	n/a	n/a
38	POLR2A	chr12:25347834-25348646	GM19193	blood:	n/a	n/a
39	POLR2A	chr12:25347727-25349494	PBDE	blood:	n/a	n/a
40	RCOR1	chr12:25347816-25348632	K562	blood:	n/a	n/a
41	POLR2A	chr12:25347870-25348622	HCT-116	colon:	n/a	n/a
42	MAX	chr12:25347926-25348743	A549	lung:	n/a	chr12:25348097-25348107
43	SIN3AK20	chr12:25347638-25348659	MCF-7	breast:	n/a	n/a
44	POLR2A	chr12:25347874-25349201	Hela-S3	cervix:	n/a	n/a
45	GTF2F1	chr12:25348085-25348880	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr12:25348440-25348590	HBMEC	blood vessel:	n/a	chr12:25348515-25348524
47	POLR2A	chr12:25347862-25348643	U87	brain:	n/a	n/a
48	CTCF	chr12:25348420-25348570	GM12873	blood:	n/a	chr12:25348515-25348524
49	POLR2A	chr12:25347996-25348557	K562	blood:	n/a	n/a
50	ZNF143	chr12:25347915-25348680	H1-hESC	embryonic stem cell:	n/a	chr12:25348313-25348331

No.	Distal block	Cell Line	Cell type
1	chr12:25346543..25348618-chr12:25402303..25405258,3	K562	blood:
2	chr12:25348080..25348611-chr17:7387325..7388145,2	Hela-S3	cervix:
3	chr10:93683014..93683556-chr12:25347907..25348654,2	NB4	blood:
4	chr12:25346725..25349884-chr12:25402144..25405058,5	K562	blood:
5	chr12:25347765..25350303-chr12:25380801..25383112,2	K562	blood:

Variant related genes	Relation type
CASC1	TF binding region
ENSG00000268076	Chromatin interaction
ENSG00000095564	Chromatin interaction
ENSG00000133703	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000181222	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10842508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10842509	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs10842511	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047826	0.85[CHB][hapmap]
rs11047880	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs11047882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11047918	1.00[CHB][hapmap]
rs12228277	0.92[CHB][hapmap]
rs12229161	0.85[CHB][hapmap]
rs12230737	1.00[CHB][hapmap]
rs12230955	0.94[ASN][1000 genomes]
rs12423489	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs12424283	0.92[CHB][hapmap]
rs12427141	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs17387444	0.88[CHD][hapmap]
rs2970532	0.92[CHB][hapmap]
rs3782188	0.85[CHB][hapmap]
rs3924649	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4356326	0.85[ASN][1000 genomes]
rs4623993	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs61763584	0.90[ASN][1000 genomes]
rs73071272	0.91[ASN][1000 genomes]
rs73073207	0.94[ASN][1000 genomes]
rs7312175	1.00[CHB][hapmap]
rs7969931	0.85[CHB][hapmap]
rs7973746	1.00[CHB][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription 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	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7979296	LYRM5	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25347200-25348600	Active TSS	Fetal Brain Female	brain
2	chr12:25347200-25349400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:25347400-25348800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:25347400-25348800	Active TSS	Muscle Satellite Cultured Cells	--
5	chr12:25347400-25349000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:25347400-25349000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr12:25347400-25349000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:25347400-25349000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr12:25347400-25349000	Active TSS	Psoas Muscle	Psoas
10	chr12:25347400-25349000	Active TSS	NHDF-Ad	bronchial
11	chr12:25347400-25349200	Active TSS	Brain Angular Gyrus	brain
12	chr12:25347400-25349200	Active TSS	K562	blood
13	chr12:25347400-25349400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:25347600-25348600	Active TSS	Thymus	Thymus
15	chr12:25347600-25348800	Active TSS	Brain Cingulate Gyrus	brain
16	chr12:25347600-25348800	Active TSS	Brain Hippocampus Middle	brain
17	chr12:25347600-25348800	Active TSS	Esophagus	oesophagus
18	chr12:25347600-25348800	Active TSS	Small Intestine	intestine
19	chr12:25347600-25349000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:25347600-25349000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr12:25347600-25349000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:25347600-25349000	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr12:25347600-25349000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:25347600-25349000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:25347600-25349000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:25347600-25349000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:25347600-25349000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:25347600-25349000	Active TSS	Aorta	Aorta
29	chr12:25347600-25349000	Active TSS	Fetal Kidney	kidney
30	chr12:25347600-25349000	Active TSS	Fetal Muscle Trunk	muscle
31	chr12:25347600-25349000	Active TSS	Left Ventricle	heart
32	chr12:25347600-25349000	Active TSS	Ovary	ovary
33	chr12:25347600-25349000	Active TSS	Pancreas	Pancrea
34	chr12:25347600-25349000	Active TSS	Rectal Smooth Muscle	rectum
35	chr12:25347600-25349000	Active TSS	Right Ventricle	heart
36	chr12:25347600-25349200	Active TSS	H1 Cell Line	embryonic stem cell
37	chr12:25347600-25349200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr12:25347600-25349200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:25347600-25349200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:25347600-25349200	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr12:25347600-25349200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:25347600-25349200	Active TSS	Colonic Mucosa	Colon
43	chr12:25347600-25349200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr12:25347600-25349200	Active TSS	Fetal Intestine Large	intestine
45	chr12:25347600-25349200	Active TSS	Fetal Stomach	stomach
46	chr12:25347600-25349200	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr12:25347600-25349200	Active TSS	Stomach Mucosa	stomach
48	chr12:25347600-25349400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:25347600-25349400	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr12:25347600-25349400	Active TSS	Right Atrium	heart

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