Variant report

Variant	rs1402275
Chromosome Location	chr12:123750895-123750896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123750456-123751523	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:123750557-123750928	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:123750836-123751019	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:123750864-123750914	NH-A	brain:	n/a
2	chr12:123750864-123750914	HCM	heart:	n/a
3	chr12:123750864-123750914	HEEpiC	esophagus:	n/a
4	chr12:123750864-123750914	HL-60	blood:	n/a
5	chr12:123750864-123750914	GM12891	blood:	n/a
6	chr12:123750864-123750914	HRCEpiC	kidney:	n/a
7	chr12:123750864-123750914	NB4	blood:	n/a
8	chr12:123750864-123750914	HepG2	liver:	n/a
9	chr12:123750864-123750914	HCPEpiC	choroid plexus:	n/a
10	chr12:123750864-123750914	Hepatocyte	liver:	n/a
11	chr12:123750864-123750914	SK-N-SH	brain:	n/a
12	chr12:123750864-123750914	RPTEC	kidney:	n/a
13	chr12:123750864-123750914	PANC-1	pancreas:	n/a
14	chr12:123750864-123750914	BJ	skin:	n/a
15	chr12:123750864-123750914	AG04450	lung:	fetal
16	chr12:123750864-123750914	SK-N-MC	brain:	n/a
17	chr12:123750864-123750914	Caco-2	colon:	n/a
18	chr12:123750864-123750914	HCT-116	colon:	n/a
19	chr12:123750864-123750914	MCF-7	breast:	n/a
20	chr12:123750864-123750914	PrEC	prostate:	n/a
21	chr12:123750864-123750914	ProgFib	skin:	n/a
22	chr12:123750864-123750914	AG09309	skin:	n/a
23	chr12:123750864-123750914	HMEC	breast:	n/a
24	chr12:123750864-123750914	Hela-S3	cervix:	n/a
25	chr12:123750864-123750914	SK-N-SH_RA	brain:	n/a
26	chr12:123750864-123750914	SKMC	muscle:	n/a
27	chr12:123750864-123750914	GM12892	blood:	n/a
28	chr12:123750864-123750914	LNCaP	prostate:	n/a
29	chr12:123750864-123750914	GM12878	blood:	n/a
30	chr12:123750864-123750914	HRPEpiC	eye:	n/a
31	chr12:123750864-123750914	Jurkat	blood:	n/a
32	chr12:123750864-123750914	HRE	kidney:	n/a
33	chr12:123750864-123750914	AG10803	skin:	n/a
34	chr12:123750864-123750914	CMK	blood:	n/a
35	chr12:123750864-123750914	H1-hESC	embryonic stem cell:	embryo
36	chr12:123750864-123750914	HCF	heart:	n/a
37	chr12:123750864-123750914	A549	lung:	n/a
38	chr12:123750864-123750914	PFSK-1	brain:	n/a
39	chr12:123750864-123750914	GM19239	blood:	n/a
40	chr12:123750864-123750914	HPAEpiC	pulmonary alveolar:	n/a
41	chr12:123750864-123750914	HIPEpiC	eye:	n/a
42	chr12:123750864-123750914	U87	brain:	n/a
43	chr12:123750864-123750914	HUVEC	blood vessel:	n/a
44	chr12:123750864-123750914	GM06990	blood:	n/a
45	chr12:123750864-123750914	HEK293	kidney:	embryo
46	chr12:123750864-123750914	AG04449	skin:	fetal
47	chr12:123750864-123750914	AoSMC	blood vessel:	n/a
48	chr12:123750864-123750914	HAEpiC	amniotic membrane:	n/a
49	chr12:123750864-123750914	SAEC	small airway:	n/a
50	chr12:123750864-123750914	AG09319	gingival:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123749224..123751190-chr12:124068264..124070353,2	MCF-7	breast:
2	chr12:123460655..123463100-chr12:123749736..123752602,2	MCF-7	breast:
3	chr12:123736848..123739836-chr12:123749677..123753155,4	K562	blood:
4	chr12:123749665..123751681-chr12:124116625..124119376,2	MCF-7	breast:
5	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235423	TF binding region
ENSG00000235423	CpG island
ENSG00000139697	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000086598	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1060105	0.93[GIH][hapmap]
rs10732573	0.82[EUR][1000 genomes]
rs10734901	0.82[EUR][1000 genomes]
rs10744149	0.85[AMR][1000 genomes]
rs10772995	0.84[AMR][1000 genomes]
rs10772998	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10773001	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10773002	0.81[GIH][hapmap];0.82[EUR][1000 genomes]
rs10773003	0.85[YRI][hapmap]
rs10773007	0.85[YRI][hapmap]
rs10773014	0.82[YRI][hapmap]
rs10846478	0.85[AMR][1000 genomes]
rs10846486	0.86[AMR][1000 genomes]
rs10846487	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10846491	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10846509	0.85[YRI][hapmap]
rs10846510	0.85[YRI][hapmap]
rs10846514	0.85[YRI][hapmap]
rs10846518	0.85[YRI][hapmap]
rs11057192	0.85[ASW][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs11057204	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11057206	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11057210	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11057223	0.85[YRI][hapmap]
rs11057240	0.85[YRI][hapmap]
rs11057250	0.85[YRI][hapmap]
rs11057266	0.85[YRI][hapmap]
rs11057273	0.82[YRI][hapmap]
rs12298826	0.93[GIH][hapmap]
rs12316131	0.93[GIH][hapmap]
rs12317452	0.85[YRI][hapmap]
rs12322888	0.93[GIH][hapmap]
rs12371973	0.85[YRI][hapmap]
rs1260294	0.84[GIH][hapmap]
rs12817892	0.85[EUR][1000 genomes]
rs12818067	0.85[EUR][1000 genomes]
rs12824957	0.96[EUR][1000 genomes]
rs12829456	0.85[EUR][1000 genomes]
rs1402274	0.85[ASW][hapmap];0.87[GIH][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs1533703	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1568427	0.84[GIH][hapmap]
rs1609520	0.84[GIH][hapmap]
rs1615694	0.85[AMR][1000 genomes]
rs1626899	0.89[AMR][1000 genomes]
rs1630693	0.88[AMR][1000 genomes]
rs1630905	0.89[AMR][1000 genomes]
rs1716156	0.82[AMR][1000 genomes]
rs1716157	0.85[ASW][hapmap];0.90[GIH][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes]
rs1716159	0.84[AMR][1000 genomes]
rs1716160	0.85[ASW][hapmap];0.93[GIH][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs1716164	0.85[ASW][hapmap];0.90[GIH][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs1716167	0.85[YRI][hapmap]
rs1716168	0.85[YRI][hapmap]
rs1716170	0.85[ASW][hapmap];0.97[GIH][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716171	0.85[ASW][hapmap];0.97[GIH][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716172	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716173	0.84[AMR][1000 genomes]
rs1716175	0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs1716176	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs1716177	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs1716182	0.83[AMR][1000 genomes]
rs1727290	0.83[AMR][1000 genomes]
rs1727300	0.84[AMR][1000 genomes]
rs1727306	0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs1727309	0.90[GIH][hapmap]
rs1727315	0.85[YRI][hapmap]
rs1727320	0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs1727323	0.85[ASW][hapmap];0.93[GIH][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs1727325	0.85[YRI][hapmap];0.85[AMR][1000 genomes]
rs1727331	0.84[GIH][hapmap]
rs1727334	0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1790086	0.85[AMR][1000 genomes]
rs1790087	0.85[AMR][1000 genomes]
rs1790089	0.83[AMR][1000 genomes]
rs1790095	0.85[ASW][hapmap];0.90[GIH][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs1790098	0.85[ASW][hapmap];0.90[GIH][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs1790099	0.85[ASW][hapmap];0.85[YRI][hapmap]
rs1790100	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs1790101	0.89[AMR][1000 genomes]
rs1790102	0.88[AMR][1000 genomes]
rs1790108	0.85[YRI][hapmap]
rs1790116	0.85[ASW][hapmap]
rs1790123	0.90[GIH][hapmap]
rs1790124	0.84[AMR][1000 genomes]
rs1790125	0.82[AMR][1000 genomes]
rs1790130	0.89[AMR][1000 genomes]
rs1790131	0.85[ASW][hapmap];0.93[GIH][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs1879380	0.97[GIH][hapmap];0.93[EUR][1000 genomes]
rs1969354	0.92[ASW][hapmap];0.90[GIH][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1980251	0.82[EUR][1000 genomes]
rs1980252	0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2049114	0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs2337934	0.92[ASW][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2682430	0.89[AMR][1000 genomes]
rs2682431	0.89[AMR][1000 genomes]
rs2682434	0.85[ASW][hapmap];0.93[GIH][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs2695478	0.90[GIH][hapmap]
rs28406193	0.93[GIH][hapmap]
rs28410096	0.85[YRI][hapmap]
rs28458312	0.93[GIH][hapmap]
rs28472704	0.93[GIH][hapmap]
rs28475177	0.85[YRI][hapmap]
rs2851436	0.84[AMR][1000 genomes]
rs2851450	0.87[AMR][1000 genomes]
rs2851451	0.86[AMR][1000 genomes]
rs28569885	0.87[GIH][hapmap]
rs28625019	0.87[GIH][hapmap]
rs28636834	0.93[GIH][hapmap]
rs28655516	0.85[YRI][hapmap]
rs28660993	0.85[YRI][hapmap]
rs28706696	0.87[GIH][hapmap]
rs2950537	0.83[AMR][1000 genomes]
rs3018098	0.83[AMR][1000 genomes]
rs3088303	0.85[YRI][hapmap]
rs34341465	0.85[EUR][1000 genomes]
rs4268544	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4372492	0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs4460848	0.81[GIH][hapmap]
rs4759371	0.92[ASW][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4759375	0.85[YRI][hapmap]
rs4759377	0.85[YRI][hapmap]
rs4759409	0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4759415	0.92[ASW][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4759416	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4759417	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4930718	0.84[GIH][hapmap]
rs58809476	0.85[EUR][1000 genomes]
rs6633	0.95[EUR][1000 genomes]
rs7304782	0.84[GIH][hapmap]
rs7313483	0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7315453	0.85[YRI][hapmap]
rs7953929	0.93[GIH][hapmap];0.92[EUR][1000 genomes]
rs7972811	0.85[YRI][hapmap]
rs941305	0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs941306	0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9795522	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers 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	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1402275	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1402275	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1402275	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1402275	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1402275	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1402275	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1402275	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
3	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
4	chr12:123736000-123752200	Strong transcription	Dnd41	blood
5	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:123736400-123752600	Strong transcription	NHLF	lung
8	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
9	chr12:123737200-123752000	Strong transcription	A549	lung
10	chr12:123738000-123751000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:123738000-123751200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:123738000-123751800	Strong transcription	Liver	Liver
13	chr12:123738000-123751800	Strong transcription	Fetal Intestine Large	intestine
14	chr12:123738000-123752000	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:123738000-123752000	Strong transcription	HUVEC	blood vessel
16	chr12:123738000-123752600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:123738000-123752800	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr12:123738200-123751800	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:123738200-123752000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr12:123738600-123752200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:123739000-123751600	Strong transcription	Placenta	Placenta
22	chr12:123739200-123751800	Strong transcription	Adipose Nuclei	Adipose
23	chr12:123739200-123752600	Weak transcription	Psoas Muscle	Psoas
24	chr12:123739200-123753000	Weak transcription	Right Atrium	heart
25	chr12:123739200-123753200	Weak transcription	Fetal Heart	heart
26	chr12:123739200-123754200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:123739400-123751800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr12:123739800-123751400	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:123739800-123752400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:123739800-123753200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:123740000-123753600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:123741000-123752200	Strong transcription	Osteobl	bone
33	chr12:123741000-123753600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:123742000-123752600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:123742400-123753400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:123742400-123754600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:123742400-123754600	Weak transcription	Small Intestine	intestine
38	chr12:123743000-123754200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:123743200-123751800	Strong transcription	Aorta	Aorta
40	chr12:123743400-123751800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:123743400-123752400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr12:123743400-123754000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:123743600-123752200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:123743600-123753600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:123743800-123752000	Strong transcription	Fetal Thymus	thymus
46	chr12:123743800-123752200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:123743800-123752600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:123743800-123752600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:123744000-123752400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:123744000-123753800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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