Variant report

Variant	rs12070248
Chromosome Location	chr1:161015711-161015712
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	CEBPB	chr1:161015454-161016769	GM12878	blood:	n/a	chr1:161016664-161016675
2	TAF1	chr1:161014931-161016367	ECC-1	luminal epithelium:	n/a	n/a
3	GABPA	chr1:161015475-161016293	HL-60	blood:	n/a	chr1:161015725-161015736
4	NFIC	chr1:161015359-161016829	GM12878	blood:	n/a	n/a
5	UBTF	chr1:161014808-161016009	K562	blood:	n/a	n/a
6	POLR2A	chr1:161014496-161017041	IMR90	lung:	n/a	n/a
7	IRF1	chr1:161014360-161016259	K562	blood:	n/a	chr1:161014773-161014787 chr1:161014776-161014790 chr1:161014770-161014784 chr1:161014779-161014793 chr1:161014777-161014790 chr1:161014775-161014789 chr1:161014779-161014789 chr1:161014773-161014794 chr1:161015569-161015582 chr1:161014771-161014791 chr1:161014765-161014785 chr1:161015780-161015794 chr1:161014777-161014790 chr1:161015568-161015588 chr1:161014769-161014783 chr1:161014772-161014781 chr1:161014774-161014785 chr1:161014777-161014790 chr1:161014777-161014791 chr1:161014779-161014790 chr1:161014778-161014795 chr1:161014780-161014791 chr1:161014773-161014783
8	ZNF143	chr1:161015053-161016075	Hela-S3	cervix:	n/a	n/a
9	CREB1	chr1:161015565-161015958	A549	lung:	n/a	n/a
10	POLR2A	chr1:161014571-161016485	HUVEC	blood vessel:	n/a	n/a
11	NFIC	chr1:161015405-161016833	GM12878	blood:	n/a	n/a
12	EGR1	chr1:161015591-161016250	ECC-1	luminal epithelium:	n/a	chr1:161015816-161015825 chr1:161015765-161015774
13	TCF7L2	chr1:161015641-161016284	HCT-116	colon:	n/a	n/a
14	TAF1	chr1:161014664-161016386	H1-neurons	neurons:	n/a	n/a
15	CREB1	chr1:161015611-161016098	H1-hESC	embryonic stem cell:	n/a	n/a
16	RCOR1	chr1:161015518-161016698	GM12878	blood:	n/a	n/a
17	YY1	chr1:161015464-161016428	GM12892	blood:	n/a	chr1:161016066-161016085 chr1:161015745-161015764 chr1:161015744-161015764 chr1:161015750-161015758 chr1:161016066-161016083 chr1:161016043-161016051 chr1:161015747-161015769 chr1:161016068-161016090 chr1:161015747-161015757 chr1:161016071-161016079 chr1:161016040-161016062
18	POLR2A	chr1:161014678-161018455	GM18505	blood:	n/a	n/a
19	POLR2A	chr1:161014748-161016402	HUVEC	blood vessel:	n/a	n/a
20	ZNF263	chr1:161015292-161016102	HEK293-T-REx	kidney:	n/a	chr1:161015540-161015549
21	ELF1	chr1:161015519-161016178	HepG2	liver:	n/a	chr1:161015815-161015828
22	YY1	chr1:161014863-161016692	SK-N-SH	brain:	n/a	chr1:161016066-161016085 chr1:161015745-161015764 chr1:161015744-161015764 chr1:161015405-161015419 chr1:161015312-161015323 chr1:161015750-161015758 chr1:161016066-161016083 chr1:161016043-161016051 chr1:161015409-161015420 chr1:161015747-161015769 chr1:161016068-161016090 chr1:161015747-161015757 chr1:161016071-161016079 chr1:161016040-161016062
23	IRF4	chr1:161015508-161016036	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:161014807-161016252	MCF-7	breast:	n/a	n/a
25	TEAD4	chr1:161015407-161016283	K562	blood:	n/a	n/a
26	CHD1	chr1:161015093-161016508	H1-hESC	embryonic stem cell:	n/a	n/a
27	YY1	chr1:161015526-161016421	HepG2	liver:	n/a	chr1:161016066-161016085 chr1:161015745-161015764 chr1:161015744-161015764 chr1:161015750-161015758 chr1:161016066-161016083 chr1:161016043-161016051 chr1:161015747-161015769 chr1:161016068-161016090 chr1:161015747-161015757 chr1:161016071-161016079 chr1:161016040-161016062
28	TBL1XR1	chr1:161015487-161016310	K562	blood:	n/a	n/a
29	CREB1	chr1:161015552-161016165	ECC-1	luminal epithelium:	n/a	n/a
30	CHD2	chr1:161014791-161016354	Hela-S3	cervix:	n/a	n/a
31	ZNF143	chr1:161015523-161016221	K562	blood:	n/a	n/a
32	GABPA	chr1:161015566-161016196	H1-hESC	embryonic stem cell:	n/a	chr1:161015725-161015736
33	POLR2A	chr1:161015437-161016540	HUVEC	blood vessel:	n/a	n/a
34	SP1	chr1:161015537-161016216	H1-hESC	embryonic stem cell:	n/a	chr1:161015784-161015793 chr1:161015782-161015794 chr1:161015783-161015793 chr1:161015783-161015792 chr1:161015782-161015794
35	RFX5	chr1:161014732-161016550	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:161014735-161016586	GM12878	blood:	n/a	n/a
37	NRF1	chr1:161014437-161016739	SK-N-SH	brain:	n/a	chr1:161015725-161015736 chr1:161015334-161015343
38	RCOR1	chr1:161014715-161016279	K562	blood:	n/a	n/a
39	TAF1	chr1:161015527-161016234	GM12891	blood:	n/a	n/a
40	YY1	chr1:161014954-161016468	A549	lung:	n/a	chr1:161016066-161016085 chr1:161015745-161015764 chr1:161015744-161015764 chr1:161015405-161015419 chr1:161015312-161015323 chr1:161015750-161015758 chr1:161016066-161016083 chr1:161016043-161016051 chr1:161015409-161015420 chr1:161015747-161015769 chr1:161016068-161016090 chr1:161015747-161015757 chr1:161016071-161016079 chr1:161016040-161016062
41	TCF12	chr1:161014925-161016199	ECC-1	luminal epithelium:	n/a	chr1:161015343-161015353
42	SIN3AK20	chr1:161014635-161015835	K562	blood:	n/a	n/a
43	E2F6	chr1:161014694-161016384	A549	lung:	n/a	chr1:161015031-161015040 chr1:161015406-161015416
44	GTF2B	chr1:161015371-161016320	K562	blood:	n/a	n/a
45	POLR2A	chr1:161014603-161018080	H1-hESC	embryonic stem cell:	n/a	n/a
46	GTF2F1	chr1:161015537-161016225	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr1:161015467-161016686	K562	blood:	n/a	chr1:161016066-161016085 chr1:161015745-161015764 chr1:161015744-161015764 chr1:161015750-161015758 chr1:161016066-161016083 chr1:161016043-161016051 chr1:161015747-161015769 chr1:161016068-161016090 chr1:161015747-161015757 chr1:161016071-161016079 chr1:161016040-161016062
48	EP300	chr1:161015576-161016911	GM12878	blood:	n/a	chr1:161016643-161016657
49	TAF1	chr1:161014895-161016159	HepG2	liver:	n/a	n/a
50	POU2F2	chr1:161015481-161016650	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:161013722..161017299-chr1:161066199..161071039,5	MCF-7	breast:
2	chr1:160990576..160992373-chr1:161014612..161018487,6	K562	blood:
3	chr1:12676672..12677659-chr1:161015482..161016373,2	Hela-S3	cervix:
4	chr1:161013470..161017562-chr1:161084888..161088962,4	MCF-7	breast:
5	chr1:161015359..161016212-chr18:23669988..23670604,2	Hela-S3	cervix:
6	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
7	chr1:161014972..161017157-chr1:161051557..161054618,4	MCF-7	breast:
8	chr1:161013542..161018278-chr1:161100825..161104206,7	MCF-7	breast:
9	chr1:161015334..161017315-chr1:161043865..161045880,2	MCF-7	breast:
10	chr1:161015709..161016480-chr9:91932957..91933732,2	Hela-S3	cervix:
11	chr1:161013435..161019346-chr1:161039308..161043996,7	MCF-7	breast:
12	chr1:161014965..161015754-chr2:63815057..63815914,2	HCT-116	colon:
13	chr1:161012196..161017661-chr1:161066183..161070852,8	MCF-7	breast:
14	chr1:161015658..161017550-chr1:161101051..161103879,2	K562	blood:
15	chr1:161015316..161018134-chr1:161085942..161088191,3	K562	blood:
16	chr1:161015575..161016271-chr1:161735870..161736519,2	Hela-S3	cervix:
17	chr1:152009359..152009873-chr1:161015206..161016187,2	Hela-S3	cervix:
18	chr1:161014200..161017793-chr1:161057956..161063190,6	MCF-7	breast:
19	chr1:161015695..161016302-chrX:85302095..85302617,2	Hela-S3	cervix:
20	chr1:161014674..161017488-chr19:12900939..12902636,2	MCF-7	breast:
21	chr1:161015644..161016480-chr20:62151701..62152619,2	Hela-S3	cervix:
22	chr1:161015188..161015839-chr15:72410047..72410840,2	Hela-S3	cervix:
23	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:
24	chr1:59249252..59250042-chr1:161015502..161016271,2	Hela-S3	cervix:
25	chr1:161013674..161020196-chr1:161084642..161090709,10	MCF-7	breast:
26	chr1:161014785..161017336-chr1:161283873..161286388,3	K562	blood:
27	chr1:161011663..161014033-chr1:161014079..161015803,2	K562	blood:
28	chr1:161014566..161017528-chr1:161100154..161103523,4	K562	blood:
29	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
30	chr1:160989721..160993044-chr1:161014364..161019082,7	K562	blood:
31	chr1:161015326..161017095-chr1:161122085..161124023,2	MCF-7	breast:
32	chr1:161013921..161016040-chr1:161036662..161039623,2	MCF-7	breast:
33	chr1:161015352..161017179-chr1:161086691..161088320,2	K562	blood:
34	chr1:36235222..36235921-chr1:161015170..161016157,2	Hela-S3	cervix:
35	chr1:161015399..161016324-chr1:161102283..161103079,2	MCF-7	breast:

Variant related genes	Relation type
USF1	TF binding region
ENSG00000066933	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000186517	Chromatin interaction
ENSG00000141380	Chromatin interaction
ENSG00000188419	Chromatin interaction
ENSG00000143222	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000177606	Chromatin interaction
ENSG00000143252	Chromatin interaction
ENSG00000092853	Chromatin interaction
ENSG00000162496	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000226889	Chromatin interaction
ENSG00000014641	Chromatin interaction
ENSG00000125534	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000143951	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000166192	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000187742	Chromatin interaction
ENSG00000158796	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10158361	1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs17181842	1.00[AMR][1000 genomes]
rs56774086	1.00[AMR][1000 genomes]
rs6703741	1.00[MEX][hapmap]
rs74124624	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12070248	CD84	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161014000-161016200	Active TSS	Muscle Satellite Cultured Cells	--
2	chr1:161014000-161016400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:161014000-161016400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:161014000-161017200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:161014200-161016400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:161014200-161016400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:161014200-161016400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:161014200-161016400	Active TSS	Fetal Muscle Trunk	muscle
9	chr1:161014200-161016400	Active TSS	Lung	lung
10	chr1:161014200-161016400	Active TSS	Pancreas	Pancrea
11	chr1:161014200-161016600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr1:161014200-161016600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr1:161014200-161016800	Active TSS	GM12878-XiMat	blood
14	chr1:161014400-161016000	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:161014400-161016000	Active TSS	Small Intestine	intestine
16	chr1:161014400-161016200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:161014400-161016200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:161014400-161016200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:161014400-161016200	Active TSS	Fetal Intestine Large	intestine
20	chr1:161014400-161016200	Active TSS	Placenta	Placenta
21	chr1:161014400-161016200	Active TSS	Stomach Mucosa	stomach
22	chr1:161014400-161016200	Active TSS	NHDF-Ad	bronchial
23	chr1:161014400-161016200	Active TSS	NHLF	lung
24	chr1:161014400-161016400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr1:161014400-161016400	Active TSS	Aorta	Aorta
26	chr1:161014400-161016400	Active TSS	Colonic Mucosa	Colon
27	chr1:161014400-161016400	Active TSS	Esophagus	oesophagus
28	chr1:161014400-161016400	Active TSS	Left Ventricle	heart
29	chr1:161014400-161016400	Active TSS	Ovary	ovary
30	chr1:161014400-161016400	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr1:161014400-161016600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:161014400-161016600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:161014400-161016600	Active TSS	Fetal Intestine Small	intestine
34	chr1:161014400-161016600	Active TSS	Fetal Kidney	kidney
35	chr1:161014400-161016600	Active TSS	Thymus	Thymus
36	chr1:161014400-161016600	Active TSS	Osteobl	bone
37	chr1:161014400-161016800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:161014400-161017000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:161014600-161016000	Active TSS	Primary monocytes fromperipheralblood	blood
40	chr1:161014600-161016000	Active TSS	Primary T cells from cord blood	blood
41	chr1:161014600-161016000	Active TSS	Primary T cells fromperipheralblood	blood
42	chr1:161014600-161016000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:161014600-161016000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:161014600-161016000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:161014600-161016000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:161014600-161016000	Active TSS	Fetal Muscle Leg	muscle
47	chr1:161014600-161016000	Active TSS	Fetal Thymus	thymus
48	chr1:161014600-161016000	Active TSS	Stomach Smooth Muscle	stomach
49	chr1:161014600-161016000	Bivalent/Poised TSS	HepG2	liver
50	chr1:161014600-161016000	Active TSS	HMEC	breast

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