Variant report

Variant	rs12268949
Chromosome Location	chr10:1104257-1104258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:1090197..1098635-chr10:1098667..1108160,39	K562	blood:
2	chr10:1041791..1044346-chr10:1102809..1104842,2	MCF-7	breast:
3	chr10:1103349..1104850-chr10:1118792..1120558,2	K562	blood:
4	chr10:1100725..1104850-chr10:1118585..1122154,6	K562	blood:
5	chr10:976791..979037-chr10:1103503..1105214,2	K562	blood:
6	chr10:975998..978434-chr10:1103106..1105638,3	MCF-7	breast:
7	chr10:1100859..1106350-chr10:1117983..1126025,11	MCF-7	breast:
8	chr10:1103509..1105162-chr10:1115825..1118791,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107929	Chromatin interaction
ENSG00000067064	Chromatin interaction
ENSG00000229869	Chromatin interaction
ENSG00000047056	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10047269	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10047382	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10047383	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10219038	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079389	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1079390	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10794720	0.92[EUR][1000 genomes]
rs11250242	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11250249	0.87[EUR][1000 genomes]
rs11250252	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11250264	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11815047	0.90[ASN][1000 genomes]
rs11816485	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11818314	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11819178	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11819230	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12247779	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12247818	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12250141	0.89[EUR][1000 genomes]
rs12359250	0.98[ASN][1000 genomes]
rs17155886	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2279256	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2387299	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2892254	0.96[ASN][1000 genomes]
rs3886474	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41299206	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56004802	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57514701	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59377495	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61571350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7071670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075830	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7093915	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100114	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74117685	0.92[EUR][1000 genomes]
rs74117831	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74117848	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74117849	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74117850	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74120451	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
rs12268949	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1100800-1104400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:1101200-1104400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:1101200-1104400	Active TSS	Right Atrium	heart
4	chr10:1101400-1104400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:1101600-1104400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr10:1102800-1104400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:1103200-1104400	Flanking Active TSS	Brain Germinal Matrix	brain
8	chr10:1103400-1104400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr10:1103400-1104400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr10:1103400-1104400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr10:1103400-1104400	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr10:1103400-1104400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr10:1103600-1104400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr10:1103600-1104400	Enhancers	Pancreas	Pancrea
15	chr10:1103600-1104400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr10:1103600-1104400	Enhancers	Small Intestine	intestine
17	chr10:1103600-1104400	Flanking Active TSS	HMEC	breast
18	chr10:1103600-1104600	Enhancers	Primary B cells from peripheral blood	blood
19	chr10:1103600-1104600	Enhancers	Spleen	Spleen
20	chr10:1103600-1105200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr10:1103600-1105800	Weak transcription	Gastric	stomach
22	chr10:1103600-1108200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr10:1103600-1109000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr10:1103600-1109600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr10:1103600-1110400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:1103600-1119400	Weak transcription	Aorta	Aorta
27	chr10:1103600-1119600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr10:1103800-1104400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr10:1103800-1104400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:1103800-1104400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:1103800-1104400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:1103800-1104400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr10:1103800-1104400	Enhancers	Fetal Muscle Leg	muscle
34	chr10:1103800-1104400	Enhancers	Ovary	ovary
35	chr10:1103800-1104400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr10:1103800-1104400	Flanking Active TSS	Right Ventricle	heart
37	chr10:1103800-1104400	Enhancers	HSMMtube	muscle
38	chr10:1103800-1104600	Enhancers	Colon Smooth Muscle	Colon
39	chr10:1103800-1104800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:1103800-1104800	Enhancers	Fetal Intestine Large	intestine
41	chr10:1103800-1105200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr10:1103800-1107000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr10:1103800-1107600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr10:1103800-1108600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr10:1103800-1108800	Weak transcription	Fetal Stomach	stomach
46	chr10:1103800-1109400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr10:1103800-1118200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr10:1104000-1104400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr10:1104000-1104400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:1104000-1104400	Enhancers	Primary hematopoietic stem cells	blood

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