Variant report

Variant	rs3738315
Chromosome Location	chr1:47903063-47903064
allele	C/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	POLR2A	chr1:47902127-47903588	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:47902800-47903644	GM12878	blood:	n/a	n/a
3	CTCF	chr1:47901969-47903966	A549	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
4	SIN3A	chr1:47902874-47903634	GM12878	blood:	n/a	chr1:47902880-47902893 chr1:47902881-47902892
5	POLR2A	chr1:47903009-47903885	MCF-7	breast:	n/a	n/a
6	CTCF	chr1:47902083-47903846	IMR90	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
7	HEY1	chr1:47903011-47903970	K562	blood:	n/a	chr1:47903782-47903797 chr1:47903546-47903561 chr1:47903130-47903145 chr1:47903317-47903332 chr1:47903405-47903420 chr1:47903760-47903775 chr1:47903646-47903661
8	TCF7L2	chr1:47902190-47903850	HCT-116	colon:	n/a	n/a
9	ELF1	chr1:47902073-47903938	K562	blood:	n/a	chr1:47903423-47903436 chr1:47903588-47903600 chr1:47903133-47903145 chr1:47903288-47903300 chr1:47903322-47903331 chr1:47903787-47903796 chr1:47903785-47903797 chr1:47903292-47903301 chr1:47903793-47903802 chr1:47903655-47903667 chr1:47903784-47903793 chr1:47903788-47903800 chr1:47903315-47903327
10	RCOR1	chr1:47901790-47903838	K562	blood:	n/a	n/a
11	POLR2A	chr1:47902754-47903955	K562	blood:	n/a	n/a
12	UBTF	chr1:47902126-47904027	K562	blood:	n/a	n/a
13	ZBTB7A	chr1:47902143-47904182	K562	blood:	n/a	chr1:47903645-47903654
14	TBP	chr1:47903047-47903955	K562	blood:	n/a	n/a
15	EGR1	chr1:47903043-47904080	HCT-116	colon:	n/a	chr1:47903693-47903708 chr1:47903694-47903707 chr1:47903657-47903667 chr1:47903691-47903705 chr1:47903692-47903702 chr1:47903695-47903705 chr1:47903694-47903707
16	CTCF	chr1:47903040-47903190	BJ	skin:	n/a	n/a
17	MAX	chr1:47902072-47903880	NB4	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
18	POLR2A	chr1:47902034-47904062	HEK293	kidney:	n/a	n/a
19	POLR2A	chr1:47902966-47903703	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:47902903-47904044	MCF-7	breast:	n/a	n/a
21	SIN3A	chr1:47902890-47903810	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:47903052-47903937	Hela-S3	cervix:	n/a	n/a
23	CHD1	chr1:47902881-47903637	GM12878	blood:	n/a	chr1:47903380-47903390
24	POLR2A	chr1:47902066-47903914	Hela-S3	cervix:	n/a	n/a
25	MAX	chr1:47902080-47904090	HepG2	liver:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
26	CREB1	chr1:47902014-47904068	HepG2	liver:	n/a	n/a
27	ELF1	chr1:47902991-47903831	K562	blood:	n/a	chr1:47903423-47903436 chr1:47903588-47903600 chr1:47903133-47903145 chr1:47903288-47903300 chr1:47903322-47903331 chr1:47903787-47903796 chr1:47903785-47903797 chr1:47903292-47903301 chr1:47903793-47903802 chr1:47903655-47903667 chr1:47903784-47903793 chr1:47903788-47903800 chr1:47903315-47903327
28	BACH1	chr1:47903013-47903914	H1-hESC	embryonic stem cell:	n/a	n/a
29	CCNT2	chr1:47902133-47904058	K562	blood:	n/a	chr1:47903693-47903702
30	POLR2A	chr1:47902971-47903893	PANC-1	pancreas:	n/a	n/a
31	MAZ	chr1:47901897-47903976	GM12878	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
32	RELA	chr1:47903025-47903687	GM15510	blood:	n/a	n/a
33	CTCF	chr1:47903020-47903170	BJ	skin:	n/a	n/a
34	CTCF	chr1:47903025-47903779	Spleen_OC	spleen:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652
35	POLR2A	chr1:47902171-47903941	NB4	blood:	n/a	n/a
36	CTCF	chr1:47903036-47903814	K562	blood:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652
37	SIN3AK20	chr1:47902531-47904036	PANC-1	pancreas:	n/a	n/a
38	MAX	chr1:47902742-47903952	A549	lung:	n/a	chr1:47903585-47903595 chr1:47903694-47903704
39	RUNX3	chr1:47902722-47903857	GM12878	blood:	n/a	n/a
40	MYC	chr1:47902116-47903922	K562	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
41	CTCF	chr1:47902758-47903820	GM12892	blood:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652
42	POLR2A	chr1:47903011-47903728	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr1:47902857-47903913	GM12878	blood:	n/a	n/a
44	MYC	chr1:47902045-47903986	K562	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
45	YY1	chr1:47902970-47903867	GM12878	blood:	n/a	chr1:47903784-47903798 chr1:47903785-47903796 chr1:47903693-47903702 chr1:47903137-47903146 chr1:47903588-47903602 chr1:47903649-47903660 chr1:47903322-47903331 chr1:47903784-47903793 chr1:47903790-47903804 chr1:47903787-47903796 chr1:47903132-47903146 chr1:47903787-47903801
46	POLR2A	chr1:47902879-47903698	GM18526	blood:	n/a	n/a
47	POLR2A	chr1:47903062-47903926	K562	blood:	n/a	n/a
48	CHD2	chr1:47902174-47903867	Hela-S3	cervix:	n/a	chr1:47903702-47903712 chr1:47903380-47903390
49	GABPA	chr1:47903028-47903920	K562	blood:	n/a	chr1:47903693-47903702 chr1:47903704-47903713
50	E2F4	chr1:47902147-47903868	K562	blood:	n/a	chr1:47903704-47903713 chr1:47903791-47903801 chr1:47902892-47902907 chr1:47903192-47903202 chr1:47903693-47903702 chr1:47903334-47903345 chr1:47903788-47903798 chr1:47903785-47903795

No.	Distal block	Cell Line	Cell type
1	chr1:47901774..47903783-chr1:47905502..47907193,2	MCF-7	breast:
2	chr1:47901790..47903824-chr1:48190200..48191775,2	K562	blood:
3	chr1:47894501..47897089-chr1:47902727..47904976,2	MCF-7	breast:
4	chr1:47902221..47904815-chr1:47929260..47931018,2	K562	blood:
5	chr1:47902573..47903219-chr14:100274224..100274724,2	Hela-S3	cervix:
6	chr1:47902455..47903363-chr10:89577216..89577997,2	Hela-S3	cervix:
7	chr1:47901999..47903599-chr1:48174794..48176429,2	MCF-7	breast:
8	chr1:47903024..47904874-chr1:47914470..47916409,2	K562	blood:
9	chr1:47902477..47903371-chr9:131218074..131218707,2	Hela-S3	cervix:
10	chr1:47902934..47903670-chr1:47913431..47914329,2	K562	blood:
11	chr1:47902862..47904142-chr1:48175786..48176848,4	K562	blood:

Variant related genes	Relation type
FOXD2-AS1	TF binding region
ENSG00000223820	Chromatin interaction
ENSG00000138138	Chromatin interaction
ENSG00000136811	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10399673	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12070024	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12090153	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1316443	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1680020	0.89[ASN][1000 genomes]
rs2405922	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2622909	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622917	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2622920	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2622921	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2820970	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2820971	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2820974	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4603175	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55718554	0.80[EUR][1000 genomes]
rs557851	0.89[ASN][1000 genomes]
rs571281	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61103903	0.87[ASN][1000 genomes]
rs6673882	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7552140	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9436899	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3432093	chr1:47901465-47906063	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv3406880	chr1:47901890-47905238	Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3738315	CMPK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47899000-47904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:47901400-47908000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
3	chr1:47901800-47903200	Flanking Active TSS	Liver	Liver
4	chr1:47901800-47903200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
5	chr1:47901800-47904000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
6	chr1:47901800-47904600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:47902000-47903200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr1:47902000-47903200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:47902000-47903200	Flanking Active TSS	HUVEC	blood vessel
10	chr1:47902000-47903600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:47902000-47904400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
12	chr1:47902000-47904400	Active TSS	A549	lung
13	chr1:47902000-47904800	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr1:47902200-47903200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr1:47902200-47903200	Flanking Active TSS	Spleen	Spleen
16	chr1:47902200-47903600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:47902200-47904000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:47902200-47904000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:47902200-47904000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
20	chr1:47902200-47904000	Active TSS	Hela-S3	cervix
21	chr1:47902200-47904200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:47902200-47904200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:47902200-47904200	Active TSS	HMEC	breast
24	chr1:47902200-47904200	Active TSS	K562	blood
25	chr1:47902200-47904400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:47902200-47904400	Active TSS	HSMM	muscle
27	chr1:47902200-47904400	Active TSS	NHLF	lung
28	chr1:47902200-47904600	Active TSS	Small Intestine	intestine
29	chr1:47902200-47905000	Active TSS	Aorta	Aorta
30	chr1:47902200-47906000	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:47902400-47903400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr1:47902400-47903400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:47902400-47903400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
34	chr1:47902400-47903600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
35	chr1:47902400-47903800	Active TSS	Esophagus	oesophagus
36	chr1:47902400-47903800	Active TSS	Dnd41	blood
37	chr1:47902400-47904000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:47902400-47904000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:47902400-47904000	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:47902400-47904400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
41	chr1:47902400-47904400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:47902400-47904400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:47902400-47904600	Bivalent Enhancer	Fetal Brain Male	brain
44	chr1:47902400-47904800	Active TSS	Ovary	ovary
45	chr1:47902600-47903200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
46	chr1:47902600-47903400	Active TSS	Thymus	Thymus
47	chr1:47902600-47903600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:47902600-47903600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:47902600-47903600	Active TSS	Brain Substantia Nigra	brain
50	chr1:47902600-47904000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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