Variant report

Variant	rs2108398
Chromosome Location	chr12:1799993-1799994
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	RUNX3	chr12:1799758-1800708	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:1799729-1800835	GM18951	blood:	n/a	n/a
3	POLR2A	chr12:1799756-1800286	GM12892	blood:	n/a	n/a
4	CHD2	chr12:1799753-1800798	Hela-S3	cervix:	n/a	chr12:1800723-1800733 chr12:1800438-1800448
5	POU2F2	chr12:1799856-1800098	GM12878	blood:	n/a	n/a
6	SP1	chr12:1799693-1800541	HCT-116	colon:	n/a	chr12:1799901-1799915
7	MXI1	chr12:1799398-1801752	SK-N-SH	brain:	n/a	n/a
8	CHD2	chr12:1799803-1800338	K562	blood:	n/a	n/a
9	ATF3	chr12:1799991-1800250	K562	blood:	n/a	n/a
10	NFIC	chr12:1799837-1800179	HepG2	liver:	n/a	n/a
11	YY1	chr12:1799945-1800240	HCT-116	colon:	n/a	n/a
12	YY1	chr12:1799784-1800677	HepG2	liver:	n/a	chr12:1799888-1799902
13	ETS1	chr12:1799854-1800218	A549	lung:	n/a	chr12:1800082-1800092 chr12:1800036-1800049 chr12:1800086-1800095 chr12:1800081-1800097 chr12:1799957-1799964 chr12:1800084-1800093 chr12:1800084-1800093 chr12:1800085-1800094 chr12:1800035-1800048
14	ELF1	chr12:1799721-1800705	MCF-7	breast:	n/a	chr12:1800084-1800095 chr12:1800085-1800094
15	SIX5	chr12:1799853-1800282	A549	lung:	n/a	n/a
16	MAFK	chr12:1799694-1800223	Hela-S3	cervix:	n/a	n/a
17	NRF1	chr12:1799914-1800270	K562	blood:	n/a	chr12:1800103-1800114
18	RCOR1	chr12:1799832-1800241	HepG2	liver:	n/a	n/a
19	POLR2A	chr12:1799737-1800342	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:1799881-1800359	HepG2	liver:	n/a	n/a
21	USF2	chr12:1799736-1800227	Hela-S3	cervix:	n/a	n/a
22	GABPA	chr12:1799942-1800281	HepG2	liver:	n/a	n/a
23	ELF1	chr12:1799561-1800426	HCT-116	colon:	n/a	chr12:1800084-1800095 chr12:1800085-1800094
24	POLR2A	chr12:1799703-1800964	HL-60	blood:	n/a	n/a
25	JUN	chr12:1799030-1801092	K562	blood:	n/a	chr12:1800125-1800134 chr12:1800811-1800823
26	POLR2A	chr12:1799753-1800943	HepG2	liver:	n/a	n/a
27	HMGN3	chr12:1799834-1800789	K562	blood:	n/a	n/a
28	YY1	chr12:1799773-1800319	SK-N-SH_RA	brain:	n/a	chr12:1799888-1799902
29	RFX5	chr12:1799973-1800293	GM12878	blood:	n/a	n/a
30	EP300	chr12:1799907-1800426	H1-hESC	embryonic stem cell:	n/a	n/a
31	IRF1	chr12:1799615-1800236	K562	blood:	n/a	chr12:1799737-1799757
32	RAD21	chr12:1799778-1800856	IMR90	lung:	n/a	chr12:1800666-1800676 chr12:1800664-1800676 chr12:1800665-1800678
33	TAF1	chr12:1799795-1800652	MCF-7	breast:	n/a	n/a
34	SREBP2	chr12:1799936-1800307	HepG2	liver:	n/a	n/a
35	MAX	chr12:1799755-1800799	H1-hESC	embryonic stem cell:	n/a	chr12:1799900-1799910 chr12:1800352-1800359
36	PML	chr12:1799823-1800275	K562	blood:	n/a	n/a
37	ETS1	chr12:1799893-1800505	GM12878	blood:	n/a	chr12:1800082-1800092 chr12:1800036-1800049 chr12:1800437-1800448 chr12:1800086-1800095 chr12:1800081-1800097 chr12:1799957-1799964 chr12:1800084-1800093 chr12:1800084-1800093 chr12:1800085-1800094 chr12:1800035-1800048
38	JUND	chr12:1799770-1800570	H1-hESC	embryonic stem cell:	n/a	chr12:1800125-1800134
39	POLR2A	chr12:1799666-1800874	GM19193	blood:	n/a	n/a
40	TCF12	chr12:1799847-1800263	A549	lung:	n/a	n/a
41	HEY1	chr12:1799641-1800709	HepG2	liver:	n/a	n/a
42	SIN3A	chr12:1799709-1801161	H1-hESC	embryonic stem cell:	n/a	chr12:1800479-1800490 chr12:1800104-1800117
43	NFIC	chr12:1799634-1800217	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:1799629-1801104	H1-hESC	embryonic stem cell:	n/a	n/a
45	SIN3AK20	chr12:1799956-1800816	PANC-1	pancreas:	n/a	n/a
46	NR3C1	chr12:1799982-1800283	A549	lung:	n/a	n/a
47	YY1	chr12:1799834-1800369	GM12892	blood:	n/a	chr12:1799888-1799902
48	ELF1	chr12:1799919-1800396	K562	blood:	n/a	chr12:1800084-1800095 chr12:1800085-1800094
49	MAZ	chr12:1799985-1800779	HepG2	liver:	n/a	chr12:1800352-1800359
50	EGR1	chr12:1799938-1800298	K562	blood:	n/a	chr12:1800175-1800189 chr12:1800036-1800060

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:1799970-1800020	NT2-D1	testis:	n/a
2	chr12:1799970-1800020	Caco-2	colon:	n/a
3	chr12:1799970-1800020	PANC-1	pancreas:	n/a
4	chr12:1799970-1800020	Hela-S3	cervix:	n/a
5	chr12:1799970-1800020	HAEpiC	amniotic membrane:	n/a
6	chr12:1799970-1800020	HepG2	liver:	n/a
7	chr12:1799970-1800020	HEEpiC	esophagus:	n/a
8	chr12:1799970-1800020	AG04449	skin:	fetal
9	chr12:1799970-1800020	MCF-7	breast:	n/a
10	chr12:1799970-1800020	HL-60	blood:	n/a
11	chr12:1799970-1800020	HCF	heart:	n/a
12	chr12:1799970-1800020	HUVEC	blood vessel:	n/a
13	chr12:1799970-1800020	RPTEC	kidney:	n/a
14	chr12:1799970-1800020	NH-A	brain:	n/a
15	chr12:1799970-1800020	SAEC	small airway:	n/a
16	chr12:1799970-1800020	HMEC	breast:	n/a
17	chr12:1799970-1800020	PFSK-1	brain:	n/a
18	chr12:1799970-1800020	BE2_C	brain:	n/a
19	chr12:1799970-1800020	NB4	blood:	n/a
20	chr12:1799970-1800020	SK-N-MC	brain:	n/a
21	chr12:1799970-1800020	AG10803	skin:	n/a
22	chr12:1799970-1800020	K562	blood:	n/a
23	chr12:1799970-1800020	SKMC	muscle:	n/a
24	chr12:1799970-1800020	U87	brain:	n/a
25	chr12:1799970-1800020	MCF10A-Er-Src	breast:	n/a
26	chr12:1799970-1800020	HCM	heart:	n/a
27	chr12:1799970-1800020	GM12891	blood:	n/a
28	chr12:1799970-1800020	HCPEpiC	choroid plexus:	n/a
29	chr12:1799970-1800020	AG09309	skin:	n/a
30	chr12:1799970-1800020	Hepatocyte	liver:	n/a
31	chr12:1799970-1800020	A549	lung:	n/a
32	chr12:1799970-1800020	HIPEpiC	eye:	n/a
33	chr12:1799970-1800020	NHBE	bronchial:	n/a
34	chr12:1799970-1800020	PrEC	prostate:	n/a
35	chr12:1799970-1800020	GM12878	blood:	n/a
36	chr12:1799970-1800020	ECC-1	luminal epithelium:	n/a
37	chr12:1799970-1800020	T-47D	breast:	n/a
38	chr12:1799970-1800020	AG04450	lung:	fetal
39	chr12:1799970-1800020	BJ	skin:	n/a
40	chr12:1799970-1800020	AoSMC	blood vessel:	n/a
41	chr12:1799970-1800020	SK-N-SH_RA	brain:	n/a
42	chr12:1799970-1800020	NHDF-neo	bronchial:	n/a
43	chr12:1799970-1800020	AG09319	gingival:	n/a
44	chr12:1799970-1800020	HRE	kidney:	n/a
45	chr12:1799970-1800020	HRPEpiC	eye:	n/a
46	chr12:1799970-1800020	GM12892	blood:	n/a
47	chr12:1799970-1800020	SK-N-SH	brain:	n/a
48	chr12:1799970-1800020	HRCEpiC	kidney:	n/a
49	chr12:1799970-1800020	IMR90	lung:	fetal
50	chr12:1799970-1800020	LNCaP	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1799823..1800792-chr6:30456838..30457762,2	Hela-S3	cervix:
2	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:
3	chr11:62608970..62609639-chr12:1799820..1800472,2	HCT-116	colon:
4	chr12:1769387..1773191-chr12:1797591..1801415,7	K562	blood:
5	chr1:235291765..235292608-chr12:1799953..1800923,2	Hela-S3	cervix:
6	chr12:1799825..1801584-chr17:59476233..59479039,2	MCF-7	breast:
7	chr1:249199693..249200680-chr12:1799951..1800891,2	Hela-S3	cervix:
8	chr12:1799819..1800546-chr8:124286478..124287091,2	Hela-S3	cervix:
9	chr11:62608460..62609387-chr12:1799892..1800891,3	Hela-S3	cervix:
10	chr12:1797794..1800188-chr12:1882818..1885035,2	MCF-7	breast:
11	chr12:1798163..1800510-chr12:1865299..1867613,2	K562	blood:
12	chr12:1768367..1774746-chr12:1797764..1801789,11	MCF-7	breast:

Variant related genes	Relation type
ADIPOR2	TF binding region
ADIPOR2	CpG island
ENSG00000185220	Chromatin interaction
ENSG00000173726	Chromatin interaction
ENSG00000266043	Chromatin interaction
ENSG00000165156	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000243663	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000204592	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11061904	1.00[EUR][1000 genomes]
rs1860049	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2041059	1.00[EUR][1000 genomes]
rs2369974	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2370054	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35510932	1.00[EUR][1000 genomes]
rs4765838	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4766411	1.00[EUR][1000 genomes]
rs4766420	1.00[EUR][1000 genomes]
rs56369812	1.00[EUR][1000 genomes]
rs6489321	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6489325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7133749	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7135229	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7136278	0.87[AFR][1000 genomes]
rs7297878	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7304843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7308757	1.00[EUR][1000 genomes]
rs7314133	1.00[EUR][1000 genomes]
rs74061311	1.00[EUR][1000 genomes]
rs74061331	1.00[EUR][1000 genomes]
rs74061332	1.00[EUR][1000 genomes]
rs758026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs758027	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs758169	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7957003	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7962777	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7964434	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription 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 miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1799200-1800000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr12:1799200-1800000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:1799200-1800800	Active TSS	Brain Germinal Matrix	brain
4	chr12:1799200-1801000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:1799200-1801000	Active TSS	Fetal Stomach	stomach
6	chr12:1799200-1801200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:1799200-1801400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:1799200-1801400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:1799200-1801400	Active TSS	Stomach Smooth Muscle	stomach
10	chr12:1799200-1801600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr12:1799200-1801600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:1799200-1801600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:1799200-1801800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr12:1799400-1800000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr12:1799400-1800000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr12:1799400-1800000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr12:1799400-1800000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:1799400-1800000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:1799400-1800000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr12:1799400-1800400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:1799400-1800800	Active TSS	Fetal Brain Male	brain
22	chr12:1799400-1801000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:1799400-1801000	Active TSS	Fetal Kidney	kidney
24	chr12:1799400-1801200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:1799400-1801200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:1799400-1801200	Active TSS	Fetal Intestine Small	intestine
27	chr12:1799400-1801400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:1799400-1801400	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr12:1799400-1801400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr12:1799400-1801400	Active TSS	Fetal Brain Female	brain
31	chr12:1799400-1801400	Active TSS	Fetal Muscle Leg	muscle
32	chr12:1799400-1801400	Active TSS	K562	blood
33	chr12:1799400-1801800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr12:1799400-1801800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:1799400-1801800	Active TSS	Psoas Muscle	Psoas
36	chr12:1799400-1801800	Active TSS	NHDF-Ad	bronchial
37	chr12:1799400-1803000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr12:1799600-1800000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr12:1799600-1800000	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr12:1799600-1800000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr12:1799600-1800000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr12:1799600-1800000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr12:1799600-1800000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:1799600-1800000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:1799600-1800000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:1799600-1800000	Flanking Active TSS	Placenta	Placenta
47	chr12:1799600-1800000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr12:1799600-1800400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:1799600-1800600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:1799600-1801000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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