Variant report

Variant	rs12120726
Chromosome Location	chr1:151417202-151417203
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr1:151416782-151417423	GM12878	blood:	n/a	chr1:151417116-151417125 chr1:151417116-151417125
2	RFX5	chr1:151416061-151417687	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr1:151416090-151417245	SK-N-SH	brain:	n/a	n/a
4	SPI1	chr1:151417002-151417325	GM12878	blood:	n/a	n/a
5	ZNF384	chr1:151417141-151417405	GM12878	blood:	n/a	n/a
6	SPI1	chr1:151417016-151417325	GM12891	blood:	n/a	n/a
7	SPI1	chr1:151416903-151417327	GM12878	blood:	n/a	n/a
8	NFIC	chr1:151416969-151417416	GM12878	blood:	n/a	n/a
9	RUNX3	chr1:151416911-151417332	GM12878	blood:	n/a	chr1:151417116-151417125 chr1:151417116-151417125

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151413939..151417832-chr1:151429782..151433498,5	K562	blood:
2	chr1:151414651..151422317-chr1:151482271..151486624,12	MCF-7	breast:
3	chr1:151402377..151405267-chr1:151416084..151418421,2	MCF-7	breast:
4	chr1:151415037..151418672-chr1:151540855..151543962,3	MCF-7	breast:
5	chr1:151416107..151417832-chr1:151431229..151433498,2	K562	blood:
6	chr1:151415530..151418373-chr1:151510570..151514579,6	MCF-7	breast:
7	chr1:151416337..151418551-chr1:151419407..151421895,2	K562	blood:
8	chr1:151416766..151418637-chr1:151510989..151514187,4	MCF-7	breast:
9	1:151411623-151426875..1:151592347-151603110	GM12878	blood:
10	1:151171193-151178589..1:151411623-151426875	GM12878	blood:
11	chr1:151393425..151395913-chr1:151415036..151417250,2	MCF-7	breast:
12	chr1:151411812..151418574-chr1:151428106..151433466,11	MCF-7	breast:
13	chr1:151414283..151420812-chr1:151481565..151487481,13	MCF-7	breast:
14	chr1:151417086..151418869-chr1:151427238..151429980,2	K562	blood:
15	chr1:151411841..151424302-chr1:151427210..151433048,24	MCF-7	breast:
16	chr1:151412036..151414559-chr1:151416954..151420193,3	MCF-7	breast:

No data

Variant related genes	Relation type
POGZ	TF binding region
ENSG00000143398	Chromatin interaction
ENSG00000206635	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10736380	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10749662	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204808	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204809	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204815	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204819	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11204824	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11578888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583968	0.88[EUR][1000 genomes]
rs11584694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589645	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11801791	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12025432	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs12029691	0.88[EUR][1000 genomes]
rs12044242	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12047617	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068166	0.88[EUR][1000 genomes]
rs12068368	0.90[EUR][1000 genomes]
rs12071705	0.90[EUR][1000 genomes]
rs12125310	0.89[EUR][1000 genomes]
rs12740875	0.90[EUR][1000 genomes]
rs12751531	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1342929	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs1887544	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs1887545	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2274533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274535	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2479379	0.88[EUR][1000 genomes]
rs2479385	0.88[EUR][1000 genomes]
rs2495380	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2864122	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118720	0.88[EUR][1000 genomes]
rs34884031	0.89[EUR][1000 genomes]
rs3748550	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs3976737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4246526	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4246527	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4364884	0.88[EUR][1000 genomes]
rs4528122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4971040	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4971042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971043	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs4971047	0.93[CEU][hapmap]
rs4971049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61818036	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61818037	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61818039	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587572	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6587573	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587577	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6587584	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs6587585	0.87[EUR][1000 genomes]
rs6684333	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs6689436	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7542776	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7546151	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs7546933	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv1811070	chr1:151403570-151433317	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12120726	SELENBP1	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151398400-151429600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:151398600-151417400	Weak transcription	Fetal Heart	heart
3	chr1:151400800-151417400	Weak transcription	Aorta	Aorta
4	chr1:151401000-151430000	Weak transcription	Esophagus	oesophagus
5	chr1:151401400-151417400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:151401600-151429200	Weak transcription	Spleen	Spleen
7	chr1:151405800-151428400	Weak transcription	Right Atrium	heart
8	chr1:151410200-151429800	Weak transcription	Lung	lung
9	chr1:151411400-151417400	Weak transcription	Gastric	stomach
10	chr1:151411400-151419600	Weak transcription	Fetal Stomach	stomach
11	chr1:151411400-151427200	Weak transcription	Right Ventricle	heart
12	chr1:151411400-151430000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:151411600-151417400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:151412600-151429200	Weak transcription	Brain Germinal Matrix	brain
15	chr1:151413600-151429800	Weak transcription	Pancreas	Pancrea
16	chr1:151413600-151430000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:151413800-151417400	Weak transcription	Psoas Muscle	Psoas
18	chr1:151413800-151418400	Weak transcription	NHLF	lung
19	chr1:151413800-151422600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:151413800-151428000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:151413800-151429400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:151413800-151429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:151414000-151417400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:151414000-151417400	Weak transcription	Ovary	ovary
25	chr1:151414000-151421200	Weak transcription	Thymus	Thymus
26	chr1:151414000-151429600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:151414200-151417400	Weak transcription	Left Ventricle	heart
28	chr1:151414200-151425400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:151414200-151430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:151414400-151417600	Weak transcription	Brain Substantia Nigra	brain
31	chr1:151414400-151418400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:151414400-151421200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:151414400-151429000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:151414400-151429400	Weak transcription	Fetal Kidney	kidney
35	chr1:151414400-151429400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:151414600-151417400	Weak transcription	Fetal Lung	lung
37	chr1:151414600-151421800	Weak transcription	Fetal Intestine Large	intestine
38	chr1:151414600-151428200	Weak transcription	Fetal Brain Female	brain
39	chr1:151414600-151429000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:151414600-151429000	Weak transcription	Small Intestine	intestine
41	chr1:151414600-151429200	Weak transcription	Fetal Brain Male	brain
42	chr1:151414600-151430400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:151414800-151418200	Weak transcription	Dnd41	blood
44	chr1:151414800-151420200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:151414800-151422600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:151414800-151427600	Weak transcription	K562	blood
47	chr1:151414800-151429600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:151415000-151419800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:151415000-151421000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr1:151415000-151423800	Weak transcription	Fetal Muscle Leg	muscle

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