Variant report

Variant	rs12359250
Chromosome Location	chr10:1096538-1096539
allele	A/C
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	BHLHE40	chr10:1096276-1096944	GM12878	blood:	n/a	n/a
2	CEBPB	chr10:1096150-1097171	K562	blood:	n/a	n/a
3	ZEB1	chr10:1096508-1096862	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:1093438-1096809	GM18505	blood:	n/a	n/a
5	CEBPB	chr10:1096485-1096905	MCF-7	breast:	n/a	n/a
6	YY1	chr10:1096512-1096773	GM12892	blood:	n/a	n/a
7	BHLHE40	chr10:1096438-1096929	HepG2	liver:	n/a	n/a
8	POLR2A	chr10:1096529-1096801	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:1096495-1096817	HCT-116	colon:	n/a	n/a
10	TBL1XR1	chr10:1095916-1096715	K562	blood:	n/a	n/a
11	MAX	chr10:1096414-1096936	MCF-7	breast:	n/a	n/a
12	CEBPB	chr10:1096518-1096886	A549	lung:	n/a	n/a
13	CHD1	chr10:1093464-1096968	IMR90	lung:	n/a	chr10:1095411-1095421 chr10:1095080-1095087 chr10:1094729-1094739 chr10:1095408-1095418
14	POLR2A	chr10:1093402-1097928	K562	blood:	n/a	n/a
15	POLR2A	chr10:1096538-1096801	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr10:1096491-1096886	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr10:1093464-1096904	GM12878	blood:	n/a	n/a
18	POLR2A	chr10:1094076-1096936	A549	lung:	n/a	n/a
19	MXI1	chr10:1096530-1096886	GM12878	blood:	n/a	n/a
20	YY1	chr10:1096531-1096706	K562	blood:	n/a	n/a
21	POLR2A	chr10:1093391-1097389	Hela-S3	cervix:	n/a	n/a
22	BHLHE40	chr10:1096043-1096938	K562	blood:	n/a	n/a
23	POLR2A	chr10:1096477-1096948	GM12878	blood:	n/a	n/a
24	POLR2A	chr10:1096482-1096846	K562	blood:	n/a	n/a
25	USF2	chr10:1096521-1096859	Hela-S3	cervix:	n/a	n/a
26	BCLAF1	chr10:1096469-1096975	GM12878	blood:	n/a	n/a
27	CEBPB	chr10:1096522-1096896	HepG2	liver:	n/a	n/a
28	SIN3A	chr10:1093563-1096883	H1-hESC	embryonic stem cell:	n/a	chr10:1094759-1094770
29	POLR2A	chr10:1093515-1097127	Hela-S3	cervix:	n/a	n/a
30	MXI1	chr10:1093541-1097006	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr10:1093593-1096958	MCF10A-Er-Src	breast:	n/a	n/a
32	NRF1	chr10:1094457-1096854	SK-N-SH	brain:	n/a	chr10:1094917-1094928 chr10:1096282-1096293
33	SIN3AK20	chr10:1096528-1096791	HepG2	liver:	n/a	n/a
34	POLR2A	chr10:1096483-1096782	HepG2	liver:	n/a	n/a
35	MAX	chr10:1096489-1096852	K562	blood:	n/a	n/a
36	MTA3	chr10:1096475-1096924	GM12878	blood:	n/a	n/a
37	GATA1	chr10:1094449-1096555	PBDE	blood:	n/a	chr10:1096261-1096271 chr10:1096263-1096270 chr10:1096261-1096270 chr10:1096258-1096274 chr10:1096263-1096270 chr10:1096263-1096270
38	BHLHE40	chr10:1096519-1096859	A549	lung:	n/a	n/a
39	CEBPB	chr10:1096516-1096906	HepG2	liver:	n/a	n/a
40	MYC	chr10:1096146-1096745	K562	blood:	n/a	n/a
41	YY1	chr10:1096533-1096746	HCT-116	colon:	n/a	n/a
42	POLR2A	chr10:1093383-1096642	PBDE	blood:	n/a	n/a
43	POLR2A	chr10:1096538-1096700	HepG2	liver:	n/a	n/a
44	CEBPB	chr10:1096524-1096879	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr10:1096443-1096802	HepG2	liver:	n/a	n/a
46	MXI1	chr10:1096202-1096843	HepG2	liver:	n/a	n/a
47	POLR2A	chr10:1096520-1096775	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr10:1096532-1096748	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr10:1093578-1097740	MCF10A-Er-Src	breast:	n/a	n/a
50	USF1	chr10:1096500-1096779	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:1090197..1098635-chr10:1098667..1108160,39	K562	blood:
2	chr10:1083077..1085466-chr10:1096305..1099633,3	MCF-7	breast:
3	chr10:1086551..1092852-chr10:1093358..1097808,14	MCF-7	breast:
4	chr10:975330..979257-chr10:1093215..1097529,5	K562	blood:
5	chr10:976200..979208-chr10:1093606..1097726,5	MCF-7	breast:
6	chr10:975330..979545-chr10:1093428..1097529,6	K562	blood:
7	chr10:976647..980794-chr10:1093154..1097319,8	MCF-7	breast:
8	chr10:1095340..1097626-chr10:1118637..1120510,2	MCF-7	breast:
9	chr10:1033990..1039615-chr10:1093691..1098446,7	MCF-7	breast:

Variant related genes	Relation type
IDI1	TF binding region
ENSG00000205740	Chromatin interaction
ENSG00000229869	Chromatin interaction
ENSG00000238924	Chromatin interaction
ENSG00000107929	Chromatin interaction
ENSG00000047056	Chromatin interaction
ENSG00000107937	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10047269	0.98[ASN][1000 genomes]
rs10047382	0.86[ASN][1000 genomes]
rs10047383	0.83[ASN][1000 genomes]
rs10219038	0.98[ASN][1000 genomes]
rs10794720	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11250242	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[ASN][1000 genomes]
rs11250252	0.98[ASN][1000 genomes]
rs11250264	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11815047	0.88[ASN][1000 genomes]
rs11818314	1.00[CHB][hapmap]
rs11819178	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11819230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12241632	1.00[CHB][hapmap];0.89[LWK][hapmap]
rs12247779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12247818	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs12268949	0.98[ASN][1000 genomes]
rs13377037	1.00[CHB][hapmap];0.89[LWK][hapmap]
rs17155821	1.00[CHB][hapmap];0.89[LWK][hapmap]
rs17155886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279256	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2892254	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793776	0.90[CHB][hapmap]
rs3793780	1.00[CHB][hapmap]
rs3793781	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap]
rs41299206	0.92[ASN][1000 genomes]
rs61571350	0.91[ASN][1000 genomes]
rs7071670	0.98[ASN][1000 genomes]
rs7075830	0.85[ASN][1000 genomes]
rs7093915	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7100114	0.98[ASN][1000 genomes]
rs74120451	0.98[ASN][1000 genomes]
rs7922760	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
3	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
12	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	30 gene(s)	inside rSNPs	diseases
14	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
16	nsv1040178	chr10:1024910-1126104	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv540410	chr10:1024910-1126104	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv894722	chr10:1058837-1274538	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS 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	25 gene(s)	inside rSNPs	diseases
19	nsv1046220	chr10:1064024-1188998	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
20	nsv894723	chr10:1073684-1259485	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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	24 gene(s)	inside rSNPs	diseases
21	nsv5532	chr10:1079499-1101700	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	nsv894724	chr10:1084942-1116294	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12359250	IDI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1093400-1096600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:1093400-1096600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:1093400-1096600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr10:1093400-1096600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr10:1093400-1096600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:1093400-1096600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:1093400-1096600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:1093400-1096600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:1093400-1096600	Active TSS	GM12878-XiMat	blood
10	chr10:1093400-1096600	Active TSS	HSMMtube	muscle
11	chr10:1093400-1096600	Active TSS	NHLF	lung
12	chr10:1093400-1096800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr10:1093400-1096800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr10:1093400-1096800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr10:1093400-1097000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr10:1093600-1096600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr10:1093600-1096600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:1093600-1096600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:1093600-1096600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:1093600-1096600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr10:1093600-1096600	Active TSS	A549	lung
22	chr10:1093600-1096600	Active TSS	HSMM	muscle
23	chr10:1093600-1097200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:1093800-1096600	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr10:1093800-1096600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:1093800-1096600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:1093800-1096600	Active TSS	Duodenum Mucosa	Duodenum
28	chr10:1093800-1096600	Active TSS	Esophagus	oesophagus
29	chr10:1093800-1096600	Active TSS	Fetal Intestine Small	intestine
30	chr10:1093800-1096600	Active TSS	Left Ventricle	heart
31	chr10:1093800-1096600	Active TSS	HMEC	breast
32	chr10:1094000-1096600	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr10:1094000-1096600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr10:1094000-1096800	Active TSS	Fetal Kidney	kidney
35	chr10:1094200-1096600	Active TSS	NH-A	brain
36	chr10:1094400-1096600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:1094400-1096600	Active TSS	Fetal Brain Male	brain
38	chr10:1094600-1096800	Active TSS	HepG2	liver
39	chr10:1094600-1097000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:1094800-1096600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr10:1095600-1096600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr10:1095600-1096800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr10:1095600-1097000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr10:1095600-1097000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr10:1095600-1097000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr10:1095800-1096800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr10:1095800-1096800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr10:1095800-1097000	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr10:1095800-1097000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr10:1095800-1097000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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