Variant report

Variant	rs12185709
Chromosome Location	chr2:209134733-209134734
allele	A/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	POLR2A	chr2:209134532-209134757	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:209134471-209134844	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:209129669..209131681-chr2:209132251..209135245,2	K562	blood:
2	chr2:209118313..209121811-chr2:209130870..209135068,6	MCF-7	breast:
3	chr2:209129671..209132812-chr2:209132994..209136144,5	MCF-7	breast:

Variant related genes	Relation type
IDH1	TF binding region
ENSG00000228380	TF binding region
ENSG00000115020	Chromatin interaction
ENSG00000138413	Chromatin interaction
ENSG00000231908	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10173938	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10174541	0.95[EUR][1000 genomes]
rs10176626	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10177810	0.82[EUR][1000 genomes]
rs10186350	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10189031	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10194539	0.95[EUR][1000 genomes]
rs10198535	0.98[EUR][1000 genomes]
rs10497897	0.95[EUR][1000 genomes]
rs10497898	0.95[EUR][1000 genomes]
rs10932260	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11885913	0.89[CEU][hapmap]
rs11898653	0.93[EUR][1000 genomes]
rs11901959	0.95[EUR][1000 genomes]
rs12475932	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694101	1.00[ASN][1000 genomes]
rs12694104	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392540	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13395304	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407268	0.82[EUR][1000 genomes]
rs13407897	0.95[EUR][1000 genomes]
rs13412043	0.95[EUR][1000 genomes]
rs1584200	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17700235	0.89[CEU][hapmap]
rs1866046	0.89[CEU][hapmap]
rs1900239	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2304545	0.84[EUR][1000 genomes]
rs2363465	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2363466	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28418905	0.84[EUR][1000 genomes]
rs4673391	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4673393	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4673394	0.90[CEU][hapmap]
rs4675748	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4675751	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66887797	0.98[EUR][1000 genomes]
rs6724208	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6725418	1.00[ASN][1000 genomes]
rs6736599	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67669827	0.95[EUR][1000 genomes]
rs67965883	0.86[EUR][1000 genomes]
rs73056463	0.95[EUR][1000 genomes]
rs7355562	0.88[EUR][1000 genomes]
rs7557303	0.95[EUR][1000 genomes]
rs7565247	1.00[ASN][1000 genomes]
rs7587752	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7592472	0.82[EUR][1000 genomes]
rs9288392	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs999890	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs999891	1.00[CEU][hapmap];0.86[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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription 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	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr2:209131800-209143200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:209132200-209134800	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr2:209132200-209134800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:209132200-209138200	Weak transcription	HSMMtube	muscle
5	chr2:209132200-209144800	Weak transcription	Aorta	Aorta
6	chr2:209132400-209134800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:209132600-209137400	Weak transcription	NHDF-Ad	bronchial
8	chr2:209132600-209137800	Weak transcription	Fetal Intestine Large	intestine
9	chr2:209132600-209138200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:209132800-209136200	Weak transcription	Brain Anterior Caudate	brain
11	chr2:209132800-209136200	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:209132800-209136200	Weak transcription	Placenta	Placenta
13	chr2:209132800-209136200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:209132800-209137000	Weak transcription	HSMM	muscle
15	chr2:209132800-209137800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:209132800-209137800	Weak transcription	A549	lung
17	chr2:209132800-209138200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:209132800-209138200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:209132800-209138200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:209132800-209138200	Weak transcription	NHLF	lung
21	chr2:209132800-209138600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:209132800-209138600	Weak transcription	Fetal Brain Male	brain
23	chr2:209132800-209140800	Weak transcription	Fetal Kidney	kidney
24	chr2:209132800-209141000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:209132800-209141200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:209132800-209142200	Weak transcription	Colonic Mucosa	Colon
27	chr2:209132800-209145000	Weak transcription	Gastric	stomach
28	chr2:209132800-209145600	Weak transcription	Stomach Mucosa	stomach
29	chr2:209132800-209147600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:209133000-209136000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:209133000-209136200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:209133000-209136200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:209133000-209136200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:209133000-209136200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:209133000-209136200	Weak transcription	HUVEC	blood vessel
36	chr2:209133000-209137800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:209133000-209138800	Weak transcription	Hela-S3	cervix
38	chr2:209133000-209138800	Weak transcription	NHEK	skin
39	chr2:209133000-209141400	Weak transcription	Fetal Heart	heart
40	chr2:209133200-209136000	Weak transcription	NH-A	brain
41	chr2:209133200-209136200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:209133200-209136200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:209133200-209136200	Weak transcription	Osteobl	bone
44	chr2:209133200-209138000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:209133200-209138000	Weak transcription	Fetal Brain Female	brain
46	chr2:209133200-209138000	Weak transcription	HMEC	breast
47	chr2:209133200-209138200	Weak transcription	Fetal Lung	lung
48	chr2:209133200-209140800	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:209133200-209141000	Weak transcription	Brain Substantia Nigra	brain
50	chr2:209133400-209136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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