Variant report

Variant	rs12620957
Chromosome Location	chr2:40006430-40006431
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	CHD2	chr2:40006019-40006610	GM12878	blood:	n/a	chr2:40006424-40006434
2	POLR2A	chr2:40006040-40006467	HepG2	liver:	n/a	n/a
3	MYC	chr2:40006134-40006508	HepG2	liver:	n/a	chr2:40006409-40006420 chr2:40006408-40006421 chr2:40006408-40006421 chr2:40006410-40006419 chr2:40006408-40006421 chr2:40006410-40006419
4	POLR2A	chr2:40005981-40006627	Hela-S3	cervix:	n/a	n/a
5	YY1	chr2:40006137-40006498	K562	blood:	n/a	n/a
6	POLR2A	chr2:40006044-40006628	A549	lung:	n/a	n/a
7	SP4	chr2:40006206-40006481	H1-hESC	embryonic stem cell:	n/a	n/a
8	BHLHE40	chr2:40006144-40006601	GM12878	blood:	n/a	n/a
9	USF1	chr2:40006052-40006660	SK-N-SH_RA	brain:	n/a	n/a
10	POU2F2	chr2:40006214-40006476	GM12878	blood:	n/a	n/a
11	MYBL2	chr2:40005835-40006817	HepG2	liver:	n/a	n/a
12	JUND	chr2:40005925-40006754	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr2:40006216-40006445	HepG2	liver:	n/a	n/a
14	MYC	chr2:40005292-40007381	K562	blood:	n/a	chr2:40006409-40006420 chr2:40006408-40006421 chr2:40006408-40006421 chr2:40006410-40006419 chr2:40006408-40006421 chr2:40006410-40006419
15	TAF1	chr2:40006048-40006604	K562	blood:	n/a	n/a
16	E2F6	chr2:40005965-40006521	A549	lung:	n/a	chr2:40006387-40006401 chr2:40006155-40006165 chr2:40006171-40006178 chr2:40006447-40006456 chr2:40006170-40006182 chr2:40006171-40006178 chr2:40006171-40006178
17	POLR2A	chr2:40005923-40006485	HepG2	liver:	n/a	n/a
18	MYC	chr2:40005981-40006730	H1-hESC	embryonic stem cell:	n/a	chr2:40006409-40006420 chr2:40006408-40006421 chr2:40006408-40006421 chr2:40006410-40006419 chr2:40006408-40006421 chr2:40006410-40006419
19	POLR2A	chr2:40006016-40006529	GM12891	blood:	n/a	n/a
20	POLR2A	chr2:40006069-40006638	K562	blood:	n/a	n/a
21	SIN3A	chr2:40005590-40006735	H1-hESC	embryonic stem cell:	n/a	chr2:40006411-40006420 chr2:40006409-40006418 chr2:40006204-40006217
22	YY1	chr2:40005906-40006468	HepG2	liver:	n/a	n/a
23	TBL1XR1	chr2:40006160-40006563	K562	blood:	n/a	n/a
24	EP300	chr2:40006287-40007407	K562	blood:	n/a	chr2:40007097-40007111
25	MYC	chr2:40005725-40006692	A549	lung:	n/a	chr2:40006409-40006420 chr2:40006408-40006421 chr2:40006408-40006421 chr2:40006410-40006419 chr2:40006408-40006421 chr2:40006410-40006419
26	YY1	chr2:40006007-40006520	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr2:40006010-40006537	GM12878	blood:	n/a	n/a
28	NFIC	chr2:40005804-40006440	HepG2	liver:	n/a	n/a
29	YY1	chr2:40005860-40006619	SK-N-SH_RA	brain:	n/a	n/a
30	TAF1	chr2:40005984-40006540	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr2:40005913-40006699	ECC-1	luminal epithelium:	n/a	chr2:40006409-40006420 chr2:40006408-40006421 chr2:40006408-40006421 chr2:40006410-40006419 chr2:40006408-40006421 chr2:40006410-40006419
32	GTF2F1	chr2:40006167-40006525	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr2:40005401-40006719	K562	blood:	n/a	n/a
34	HA-E2F1	chr2:40006002-40006601	Hela-S3	cervix:	n/a	chr2:40006387-40006401 chr2:40006155-40006165 chr2:40006171-40006178 chr2:40006447-40006456 chr2:40006170-40006182 chr2:40006171-40006178 chr2:40006171-40006178
35	TBP	chr2:40005560-40006912	K562	blood:	n/a	n/a
36	MXI1	chr2:40005527-40006432	Hela-S3	cervix:	n/a	chr2:40006409-40006418
37	POLR2A	chr2:40005882-40006658	GM12892	blood:	n/a	n/a
38	USF1	chr2:40005941-40006593	A549	lung:	n/a	n/a
39	STAT1	chr2:40005914-40006555	GM12878	blood:	n/a	n/a
40	USF1	chr2:40005980-40006757	SK-N-SH	brain:	n/a	n/a
41	CHD2	chr2:40006148-40006579	H1-hESC	embryonic stem cell:	n/a	chr2:40006424-40006434
42	USF2	chr2:40005991-40006871	H1-hESC	embryonic stem cell:	n/a	chr2:40006408-40006419
43	PML	chr2:40006100-40006604	MCF-7	breast:	n/a	n/a
44	BHLHE40	chr2:40006244-40006476	A549	lung:	n/a	n/a
45	ZNF143	chr2:40006119-40006902	H1-hESC	embryonic stem cell:	n/a	n/a
46	HA-E2F1	chr2:40005880-40006917	MCF-7	breast:	n/a	chr2:40006387-40006401 chr2:40006155-40006165 chr2:40006171-40006178 chr2:40006447-40006456 chr2:40006170-40006182 chr2:40006171-40006178 chr2:40006171-40006178
47	CHD1	chr2:40005853-40006450	GM12878	blood:	n/a	chr2:40006424-40006434
48	YY1	chr2:40006112-40006505	GM12891	blood:	n/a	n/a
49	POLR2A	chr2:40005768-40006797	GM18505	blood:	n/a	n/a
50	TAF1	chr2:40006178-40006477	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:105957090..105957996-chr2:40006019..40006535,2	Hela-S3	cervix:
2	chr2:39739040..39741917-chr2:40004865..40006467,2	K562	blood:

Variant related genes	Relation type
THUMPD2	TF binding region
ENSG00000185347	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10164984	0.88[EUR][1000 genomes]
rs10169390	0.92[EUR][1000 genomes]
rs10174709	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10206408	0.81[EUR][1000 genomes]
rs1035138	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1035139	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11124691	0.80[EUR][1000 genomes]
rs11124692	0.84[EUR][1000 genomes]
rs12470473	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12617624	0.84[EUR][1000 genomes]
rs12623462	0.83[ASN][1000 genomes]
rs12623545	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12624217	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12712656	0.88[EUR][1000 genomes]
rs13026313	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13400213	0.82[EUR][1000 genomes]
rs13425906	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13428837	0.88[EUR][1000 genomes]
rs1548877	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17478972	0.88[EUR][1000 genomes]
rs1986876	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2192685	0.84[EUR][1000 genomes]
rs2373689	0.84[ASN][1000 genomes]
rs35761077	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732121	0.84[ASN][1000 genomes]
rs3732122	0.82[ASN][1000 genomes]
rs4670955	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4670957	0.81[EUR][1000 genomes]
rs4670958	0.81[EUR][1000 genomes]
rs4670959	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59756273	0.84[ASN][1000 genomes]
rs6719179	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6747842	0.80[ASN][1000 genomes]
rs727376	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7560642	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7581406	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs917960	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9309042	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs997976	0.84[ASN][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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12620957	ENSG00000138050	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40001000-40006600	Active TSS	GM12878-XiMat	blood
2	chr2:40004200-40006600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:40004200-40006600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:40004200-40006600	Active TSS	HSMMtube	muscle
5	chr2:40004200-40008800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:40004400-40006600	Active TSS	HMEC	breast
7	chr2:40004400-40007000	Active TSS	Aorta	Aorta
8	chr2:40004400-40007200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr2:40004600-40006600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr2:40004600-40006600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:40004600-40006600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:40004600-40006600	Active TSS	Brain Anterior Caudate	brain
13	chr2:40004600-40006600	Active TSS	Fetal Intestine Large	intestine
14	chr2:40004600-40006600	Active TSS	Fetal Thymus	thymus
15	chr2:40004600-40006600	Active TSS	Right Ventricle	heart
16	chr2:40004600-40006800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr2:40004600-40006800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:40004600-40007000	Active TSS	Psoas Muscle	Psoas
19	chr2:40004800-40006600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:40004800-40006600	Active TSS	Fetal Intestine Small	intestine
21	chr2:40004800-40006600	Active TSS	Fetal Muscle Leg	muscle
22	chr2:40004800-40006600	Active TSS	Fetal Stomach	stomach
23	chr2:40004800-40006600	Active TSS	Stomach Smooth Muscle	stomach
24	chr2:40004800-40006600	Active TSS	NHEK	skin
25	chr2:40004800-40007000	Active TSS	Fetal Brain Female	brain
26	chr2:40004800-40007000	Active TSS	Ovary	ovary
27	chr2:40004800-40007000	Active TSS	NHLF	lung
28	chr2:40004800-40007200	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr2:40005000-40006600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr2:40005000-40006600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:40005000-40006600	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr2:40005000-40006600	Active TSS	HSMM	muscle
33	chr2:40005000-40006800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:40005000-40006800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:40005000-40007000	Active TSS	Right Atrium	heart
36	chr2:40005200-40006600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:40005200-40006600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr2:40005200-40006600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:40005200-40006600	Active TSS	Colon Smooth Muscle	Colon
40	chr2:40005200-40006600	Active TSS	Rectal Smooth Muscle	rectum
41	chr2:40005200-40006600	Active TSS	Hela-S3	cervix
42	chr2:40005200-40006600	Active TSS	K562	blood
43	chr2:40005200-40006800	Active TSS	Brain Cingulate Gyrus	brain
44	chr2:40005200-40007000	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr2:40005200-40007000	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr2:40005200-40007000	Active TSS	Fetal Muscle Trunk	muscle
47	chr2:40005200-40007000	Active TSS	Stomach Mucosa	stomach
48	chr2:40005400-40006600	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr2:40005400-40006600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:40005400-40006600	Active TSS	Muscle Satellite Cultured Cells	--

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