Variant report

Variant	rs1730128
Chromosome Location	chr2:97619913-97619914
allele	A/G
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	ATF2	chr2:97619855-97620550	GM12878	blood:	n/a	n/a
2	RUNX3	chr2:97619825-97620792	GM12878	blood:	n/a	n/a
3	EP300	chr2:97619906-97620523	GM12878	blood:	n/a	chr2:97620217-97620231
4	EBF1	chr2:97619901-97620325	GM12878	blood:	n/a	chr2:97620234-97620243 chr2:97620234-97620244
5	TCF3	chr2:97619864-97620266	GM12878	blood:	n/a	chr2:97620154-97620168
6	FOXM1	chr2:97619870-97620666	GM12878	blood:	n/a	n/a
7	WRNIP1	chr2:97619721-97620162	GM12878	blood:	n/a	n/a
8	PML	chr2:97619842-97620660	GM12878	blood:	n/a	chr2:97620474-97620482
9	ELF1	chr2:97619676-97620362	GM12878	blood:	n/a	n/a
10	EGR1	chr2:97619912-97620183	GM12878	blood:	n/a	chr2:97620062-97620076
11	BATF	chr2:97619898-97620936	GM12878	blood:	n/a	n/a
12	EBF1	chr2:97619885-97620494	GM12878	blood:	n/a	chr2:97620234-97620243 chr2:97620234-97620244
13	RELA	chr2:97619860-97620433	GM19099	blood:	n/a	n/a
14	RUNX3	chr2:97619842-97620664	GM12878	blood:	n/a	n/a
15	MTA3	chr2:97619887-97620602	GM12878	blood:	n/a	n/a
16	YY1	chr2:97619902-97620297	GM12878	blood:	n/a	n/a
17	NFIC	chr2:97619846-97620636	GM12878	blood:	n/a	chr2:97620379-97620396 chr2:97620380-97620396

No.	Distal block	Cell Line	Cell type
1	chr2:97558219..97561795-chr2:97617145..97620359,3	K562	blood:
2	chr2:97512699..97516587-chr2:97618220..97621285,3	MCF-7	breast:
3	chr2:97612976..97616193-chr2:97618171..97621254,3	K562	blood:
4	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
5	chr2:97426031..97428759-chr2:97617125..97619977,2	MCF-7	breast:
6	chr2:97521500..97526453-chr2:97614513..97620136,8	K562	blood:
7	chr2:97619225..97621126-chr2:97623559..97626363,2	K562	blood:

Variant related genes	Relation type
FAM178B	TF binding region
ENSG00000168758	Chromatin interaction
ENSG00000158158	Chromatin interaction
ENSG00000213337	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10202644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1257000	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1257008	0.96[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1257009	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1257011	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1257012	0.96[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1257015	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1257016	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1257017	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1257018	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1257019	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1257020	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1257027	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1257028	0.96[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1257029	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1268682	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12717785	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12717786	0.87[EUR][1000 genomes]
rs12717787	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13016654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13021723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1623881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624844	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1730106	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1730111	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1730119	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1730120	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1730122	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1730123	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1730124	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1730126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1730127	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1730129	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1730130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1730131	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1796027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796029	0.96[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1796032	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1796038	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1796041	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1796044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796046	1.00[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1796047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796049	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2707304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34434950	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34895357	0.81[AMR][1000 genomes]
rs4263148	0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4366944	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4586672	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6576992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576993	0.90[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576995	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576997	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6576999	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6707255	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714860	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6715329	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6725927	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6757916	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7569434	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7584318	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7584335	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7593493	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7597743	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv32727	chr2:97616488-97643975	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97612800-97620200	Enhancers	K562	blood
2	chr2:97615400-97621800	Enhancers	Colonic Mucosa	Colon
3	chr2:97615600-97620800	Enhancers	Fetal Brain Male	brain
4	chr2:97615600-97620800	Enhancers	Ovary	ovary
5	chr2:97615800-97620800	Enhancers	Fetal Lung	lung
6	chr2:97616000-97620800	Enhancers	Fetal Thymus	thymus
7	chr2:97617000-97620600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:97617000-97621800	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr2:97617000-97622800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:97617200-97620200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:97617200-97620400	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:97617200-97620400	Enhancers	Brain Hippocampus Middle	brain
13	chr2:97617200-97620600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr2:97617200-97621600	Enhancers	Placenta	Placenta
15	chr2:97617400-97620800	Enhancers	Adipose Nuclei	Adipose
16	chr2:97617400-97623400	Enhancers	Fetal Stomach	stomach
17	chr2:97617800-97620000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:97618000-97620200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:97618000-97620400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr2:97618200-97620200	Enhancers	Primary hematopoietic stem cells	blood
21	chr2:97618200-97620200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:97618200-97620800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:97618400-97620200	Enhancers	Brain Germinal Matrix	brain
24	chr2:97618400-97620400	Enhancers	Brain Angular Gyrus	brain
25	chr2:97618400-97620400	Enhancers	Fetal Kidney	kidney
26	chr2:97618400-97620600	Enhancers	Brain Substantia Nigra	brain
27	chr2:97618400-97620600	Enhancers	Fetal Brain Female	brain
28	chr2:97618400-97620800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:97618800-97620200	Enhancers	Esophagus	oesophagus
30	chr2:97618800-97620200	Enhancers	Pancreas	Pancrea
31	chr2:97618800-97620200	Enhancers	Placenta Amnion	Placenta Amnion
32	chr2:97618800-97620600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:97618800-97620800	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr2:97619000-97620200	Enhancers	Lung	lung
35	chr2:97619000-97620200	Enhancers	Right Ventricle	heart
36	chr2:97619000-97620400	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr2:97619000-97620400	Enhancers	HSMMtube	muscle
38	chr2:97619000-97620800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:97619000-97620800	Enhancers	Fetal Muscle Leg	muscle
40	chr2:97619000-97621000	Enhancers	Spleen	Spleen
41	chr2:97619200-97620400	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr2:97619200-97620800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:97619200-97620800	Enhancers	Right Atrium	heart
44	chr2:97619200-97621000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:97619200-97622200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:97619400-97620200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:97619400-97620200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:97619400-97620200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:97619400-97620200	Enhancers	Gastric	stomach
50	chr2:97619400-97620200	Enhancers	Left Ventricle	heart

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