Variant report

Variant	rs4232
Chromosome Location	chr15:59931131-59931132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59923114..59927076-chr15:59929959..59933582,4	K562	blood:
2	chr15:59930931..59933586-chr15:59938114..59940127,3	K562	blood:
3	chr15:59923114..59927076-chr15:59930243..59933582,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BNIP2-1	chr15:59931058-59931356	NONHSAT044183

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1002181	0.81[EUR][1000 genomes]
rs10152209	1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10152414	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10152415	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10162629	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1046053	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10519039	0.82[YRI][hapmap]
rs1057059	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11071465	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11071468	0.83[EUR][1000 genomes]
rs11071469	0.83[EUR][1000 genomes]
rs1135148	0.81[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11634067	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11853610	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11854063	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12441240	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593480	0.83[EUR][1000 genomes]
rs12708458	0.85[EUR][1000 genomes]
rs12708459	0.86[EUR][1000 genomes]
rs12902582	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902774	0.86[EUR][1000 genomes]
rs12906392	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12907554	0.81[EUR][1000 genomes]
rs12910751	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1479885	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531638	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1531639	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1552031	1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs16941648	0.85[YRI][hapmap]
rs17236804	0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs1871500	0.82[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2101019	0.82[CEU][hapmap]
rs2170062	0.80[EUR][1000 genomes]
rs2306354	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2306355	0.94[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306357	0.95[JPT][hapmap];0.86[YRI][hapmap]
rs2307272	0.82[EUR][1000 genomes]
rs2307275	0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes]
rs2414638	0.81[EUR][1000 genomes]
rs28671744	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3087328	0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs34797071	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34894301	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4533213	0.80[EUR][1000 genomes]
rs4774340	1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4774341	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4775191	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775195	0.88[ASW][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4775197	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151446	0.94[JPT][hapmap];0.86[YRI][hapmap]
rs6151447	0.95[JPT][hapmap];0.86[YRI][hapmap]
rs6151448	0.95[JPT][hapmap];0.84[YRI][hapmap]
rs6151449	0.95[JPT][hapmap];0.86[YRI][hapmap]
rs6151450	1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6151458	1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs6151460	0.80[EUR][1000 genomes]
rs6151461	0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes]
rs6151462	0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes]
rs6151467	0.80[EUR][1000 genomes]
rs6151470	0.80[EUR][1000 genomes]
rs6151474	0.80[EUR][1000 genomes]
rs6151477	0.80[EUR][1000 genomes]
rs6151486	0.80[EUR][1000 genomes]
rs6151496	1.00[JPT][hapmap];0.91[YRI][hapmap]
rs6151503	0.81[EUR][1000 genomes]
rs6151504	1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs6151506	0.81[EUR][1000 genomes]
rs6151514	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6151528	0.82[EUR][1000 genomes]
rs6151529	1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs6151532	1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs6151533	1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs6151535	0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs6151536	1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs6151542	0.83[EUR][1000 genomes]
rs6151545	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6151568	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151571	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151574	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151580	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151581	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151586	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151588	0.88[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151589	0.82[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151590	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62012358	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62015289	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6494127	0.81[EUR][1000 genomes]
rs6494128	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6494130	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494131	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494133	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs67820349	0.82[EUR][1000 genomes]
rs7162964	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs7164756	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172270	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7178050	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7180408	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182962	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs722163	0.80[EUR][1000 genomes]
rs722164	0.80[EUR][1000 genomes]
rs754642	0.94[JPT][hapmap]
rs8025415	0.86[YRI][hapmap]
rs8027679	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033161	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8035465	0.83[EUR][1000 genomes]
rs8041394	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer 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 target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4232	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL
rs4232	GTF2A2	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59905200-59931600	Weak transcription	Fetal Stomach	stomach
2	chr15:59905200-59946200	Weak transcription	Gastric	stomach
3	chr15:59912000-59932600	Weak transcription	Colonic Mucosa	Colon
4	chr15:59912200-59935000	Weak transcription	Fetal Intestine Small	intestine
5	chr15:59914800-59937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:59920600-59947000	Weak transcription	Small Intestine	intestine
7	chr15:59925000-59936800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:59925000-59936800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:59925000-59943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:59925400-59937200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:59925600-59936600	Weak transcription	NHLF	lung
12	chr15:59925600-59937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:59925600-59948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:59925800-59936600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:59925800-59943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:59926000-59932200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:59926200-59932600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:59926200-59936800	Weak transcription	Fetal Brain Male	brain
19	chr15:59926200-59937000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:59926400-59935800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:59926400-59936600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:59926600-59936600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:59926600-59944000	Weak transcription	Fetal Kidney	kidney
24	chr15:59926600-59947600	Weak transcription	Right Ventricle	heart
25	chr15:59926600-59948000	Weak transcription	Brain Angular Gyrus	brain
26	chr15:59927000-59937000	Weak transcription	Lung	lung
27	chr15:59927200-59936600	Weak transcription	HMEC	breast
28	chr15:59927200-59948800	Weak transcription	Aorta	Aorta
29	chr15:59927400-59943800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:59927600-59931400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr15:59927600-59933000	Strong transcription	A549	lung
32	chr15:59927600-59933800	Weak transcription	NHDF-Ad	bronchial
33	chr15:59927600-59936200	Weak transcription	Pancreas	Pancrea
34	chr15:59927800-59942800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:59928000-59932400	Strong transcription	Fetal Muscle Leg	muscle
36	chr15:59928000-59934600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:59928200-59931600	Strong transcription	Primary T cells from cord blood	blood
38	chr15:59928200-59934600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:59928200-59934600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:59928400-59932400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:59928400-59932800	Strong transcription	Left Ventricle	heart
42	chr15:59928400-59932800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr15:59928400-59933600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr15:59928400-59934400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:59928400-59934800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:59928400-59935000	Strong transcription	Primary B cells from cord blood	blood
47	chr15:59928400-59936600	Weak transcription	Brain Anterior Caudate	brain
48	chr15:59928400-59940200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:59928400-59945600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:59928600-59932400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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