Variant report

Variant	rs12619490
Chromosome Location	chr2:96927108-96927109
allele	A/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	HNF4A	chr2:96926908-96927667	HepG2	liver:	n/a	chr2:96927434-96927449
2	NFIC	chr2:96927062-96927701	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:96927069-96927715	HepG2	liver:	n/a	n/a
4	SP1	chr2:96926953-96927788	HepG2	liver:	n/a	chr2:96927202-96927223
5	CTCF	chr2:96926098-96927116	HCT-116	colon:	n/a	chr2:96926838-96926856 chr2:96926284-96926292 chr2:96926626-96926644 chr2:96926621-96926642 chr2:96926833-96926854 chr2:96926631-96926639
6	BHLHE40	chr2:96926224-96927305	K562	blood:	n/a	n/a
7	POLR2A	chr2:96925506-96927331	K562	blood:	n/a	n/a
8	FOXA2	chr2:96925423-96927270	HepG2	liver:	n/a	n/a
9	MBD4	chr2:96925917-96927742	HepG2	liver:	n/a	n/a
10	CTCF	chr2:96925805-96927208	SK-N-SH	brain:	n/a	chr2:96926838-96926856 chr2:96926284-96926292 chr2:96926626-96926644 chr2:96926621-96926642 chr2:96926833-96926854 chr2:96926631-96926639
11	HEY1	chr2:96925897-96927669	HepG2	liver:	n/a	n/a
12	MAFK	chr2:96926131-96927637	HepG2	liver:	n/a	chr2:96926794-96926809
13	MYBL2	chr2:96925742-96927800	HepG2	liver:	n/a	n/a
14	SMARCC1	chr2:96925882-96927132	Hela-S3	cervix:	n/a	chr2:96926353-96926362 chr2:96926354-96926363
15	RFX5	chr2:96925862-96927592	HepG2	liver:	n/a	chr2:96926831-96926839
16	NFYA	chr2:96926157-96927152	Hela-S3	cervix:	n/a	n/a
17	ARID3A	chr2:96925925-96927704	HepG2	liver:	n/a	n/a
18	HDAC2	chr2:96926849-96927678	HepG2	liver:	n/a	n/a
19	SMC3	chr2:96927087-96927631	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:96925974-96927604	HepG2	liver:	n/a	n/a
21	MYBL2	chr2:96925401-96927705	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:96926960-96927712	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:96926999-96927319	K562	blood:	n/a	n/a
24	ELF1	chr2:96925917-96927146	HCT-116	colon:	n/a	chr2:96926799-96926810
25	HNF4G	chr2:96926804-96927659	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96923812..96929557-chr2:96929618..96934014,11	K562	blood:
2	chr2:96804451..96805110-chr2:96926335..96927296,3	MCF-7	breast:
3	chr2:96873130..96877842-chr2:96924423..96928437,5	K562	blood:
4	chr2:96911457..96914328-chr2:96926572..96928354,2	MCF-7	breast:
5	chr2:96874408..96876271-chr2:96925161..96927177,2	K562	blood:
6	chr2:96925245..96927615-chr2:96969806..96971741,2	MCF-7	breast:
7	chr2:96925642..96927214-chr2:97001032..97003514,2	K562	blood:
8	chr2:96873368..96875940-chr2:96925082..96928161,5	MCF-7	breast:
9	chr2:96872598..96876007-chr2:96924059..96928423,13	MCF-7	breast:
10	chr2:96802971..96805127-chr2:96925819..96928248,3	MCF-7	breast:

Variant related genes	Relation type
CIAO1	TF binding region
TMEM127	TF binding region
ENSG00000135956	Chromatin interaction
ENSG00000121152	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000144028	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000188886	Chromatin interaction
ENSG00000084090	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12611936	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12612136	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12614113	1.00[AMR][1000 genomes]
rs12614623	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12616326	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619114	1.00[AMR][1000 genomes]
rs12619573	1.00[AMR][1000 genomes]
rs12619919	1.00[AMR][1000 genomes]
rs12620576	1.00[AMR][1000 genomes]
rs12620768	1.00[AMR][1000 genomes]
rs12621163	1.00[AMR][1000 genomes]
rs12621619	1.00[AMR][1000 genomes]
rs12621688	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2276647	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2290908	1.00[AMR][1000 genomes]
rs3813659	1.00[AMR][1000 genomes]
rs3813660	1.00[AMR][1000 genomes]
rs56742757	0.96[ASN][1000 genomes]
rs57213829	1.00[AMR][1000 genomes]
rs57248244	1.00[ASN][1000 genomes]
rs57319731	1.00[AMR][1000 genomes]
rs57367779	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57477571	1.00[AMR][1000 genomes]
rs58132887	1.00[AMR][1000 genomes]
rs58152078	1.00[AMR][1000 genomes]
rs59168739	1.00[AMR][1000 genomes]
rs59525841	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59621486	1.00[AMR][1000 genomes]
rs59911784	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59939559	1.00[AMR][1000 genomes]
rs60013962	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60020980	1.00[AMR][1000 genomes]
rs60302421	1.00[AMR][1000 genomes]
rs60596893	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60893927	1.00[AMR][1000 genomes]
rs61096003	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 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	chr2:96914400-96929800	Strong transcription	Fetal Stomach	stomach
2	chr2:96916000-96929400	Strong transcription	Dnd41	blood
3	chr2:96917400-96929600	Strong transcription	Brain Germinal Matrix	brain
4	chr2:96918200-96929400	Weak transcription	Fetal Brain Male	brain
5	chr2:96918200-96929600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:96920200-96928000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr2:96920200-96930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:96920600-96927400	Weak transcription	Fetal Lung	lung
9	chr2:96921000-96927800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:96921000-96929800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:96921200-96929800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:96921200-96930200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:96921800-96927200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:96921800-96930200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:96922200-96928400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr2:96922600-96927600	Genic enhancers	Fetal Muscle Leg	muscle
17	chr2:96922600-96927800	Enhancers	Left Ventricle	heart
18	chr2:96922600-96927800	Enhancers	Psoas Muscle	Psoas
19	chr2:96922600-96928400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:96922800-96927200	Enhancers	Primary hematopoietic stem cells	blood
21	chr2:96923000-96927400	Enhancers	Primary B cells from cord blood	blood
22	chr2:96923000-96928400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr2:96923400-96927400	Genic enhancers	Lung	lung
24	chr2:96923400-96929600	Strong transcription	Fetal Brain Female	brain
25	chr2:96923600-96927200	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr2:96923600-96927600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr2:96923600-96928400	Genic enhancers	Fetal Intestine Small	intestine
28	chr2:96923800-96927200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:96923800-96927400	Genic enhancers	Brain Anterior Caudate	brain
30	chr2:96923800-96927600	Genic enhancers	Placenta	Placenta
31	chr2:96923800-96927800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:96923800-96927800	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr2:96923800-96927800	Genic enhancers	Primary T cells from cord blood	blood
34	chr2:96923800-96927800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:96923800-96928000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:96923800-96928200	Genic enhancers	Spleen	Spleen
37	chr2:96923800-96928200	Enhancers	NHDF-Ad	bronchial
38	chr2:96923800-96928400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:96923800-96928800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:96923800-96929400	Enhancers	Right Atrium	heart
41	chr2:96923800-96930600	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr2:96924000-96927600	Enhancers	Ovary	ovary
43	chr2:96924000-96927800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:96924000-96928400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:96924000-96929200	Strong transcription	Thymus	Thymus
46	chr2:96924200-96927800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:96924200-96927800	Genic enhancers	HSMM	muscle
48	chr2:96924200-96929800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:96924400-96930200	Enhancers	Pancreas	Pancrea
50	chr2:96924600-96927600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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