Variant report

Variant	rs2274127
Chromosome Location	chr1:150252984-150252985
allele	A/C/G/T
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	HEY1	chr1:150252736-150253083	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:150252786-150253077	HepG2	liver:	n/a	n/a
3	HNF4A	chr1:150252763-150253093	HepG2	liver:	n/a	chr1:150252929-150252941 chr1:150252928-150252941 chr1:150252929-150252942 chr1:150252928-150252943 chr1:150252930-150252942 chr1:150252929-150252941 chr1:150252924-150252946 chr1:150252928-150252942 chr1:150252929-150252941 chr1:150252889-150252904 chr1:150252928-150252941 chr1:150252928-150252941 chr1:150252926-150252944
4	POLR2A	chr1:150252831-150253018	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:150252697-150253103	HepG2	liver:	n/a	n/a
6	EP300	chr1:150252699-150253103	HepG2	liver:	n/a	chr1:150252990-150253004 chr1:150252734-150252743 chr1:150252735-150252744
7	HDAC2	chr1:150252677-150253052	HepG2	liver:	n/a	n/a
8	YY1	chr1:150252649-150253036	HepG2	liver:	n/a	n/a
9	HNF4G	chr1:150252727-150253077	HepG2	liver:	n/a	chr1:150252929-150252941 chr1:150252926-150252941 chr1:150252928-150252941 chr1:150252929-150252942 chr1:150252928-150252943 chr1:150252930-150252942 chr1:150252929-150252941 chr1:150252924-150252946 chr1:150252928-150252942 chr1:150252929-150252941 chr1:150252889-150252904 chr1:150252928-150252941 chr1:150252928-150252941 chr1:150252926-150252944
10	HEY1	chr1:150252681-150253074	HepG2	liver:	n/a	n/a
11	HNF4A	chr1:150252687-150253026	HepG2	liver:	n/a	chr1:150252929-150252941 chr1:150252928-150252941 chr1:150252929-150252942 chr1:150252928-150252943 chr1:150252930-150252942 chr1:150252929-150252941 chr1:150252924-150252946 chr1:150252928-150252942 chr1:150252929-150252941 chr1:150252889-150252904 chr1:150252928-150252941 chr1:150252928-150252941 chr1:150252926-150252944
12	MAX	chr1:150252633-150253204	HepG2	liver:	n/a	chr1:150252735-150252744 chr1:150252734-150252743
13	POLR2A	chr1:150252795-150253053	HepG2	liver:	n/a	n/a
14	TBP	chr1:150252832-150253029	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150245244..150248880-chr1:150251272..150253316,4	K562	blood:
2	chr1:150207034..150209867-chr1:150251521..150254901,4	MCF-7	breast:
3	chr1:150252708..150255493-chr1:150334761..150336728,2	K562	blood:
4	chr1:150208242..150210612-chr1:150252083..150254317,2	K562	blood:
5	chr1:150252847..150256677-chr1:150333609..150339009,8	MCF-7	breast:
6	chr1:149856618..149859874-chr1:150252392..150257192,4	MCF-7	breast:
7	chr1:150206509..150210612-chr1:150251950..150254898,4	K562	blood:
8	chr1:150252939..150254457-chr1:150336461..150338463,2	MCF-7	breast:
9	chr1:150252171..150257673-chr1:150291650..150295636,15	MCF-7	breast:
10	chr1:150246450..150248779-chr1:150251520..150254627,3	K562	blood:
11	chr1:150226746..150229990-chr1:150252728..150255652,4	K562	blood:
12	chr1:150205879..150210456-chr1:150251557..150256195,8	MCF-7	breast:

Variant related genes	Relation type
C1orf51	TF binding region
ENSG00000184260	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000271845	Chromatin interaction
ENSG00000118298	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10788873	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1097067	0.81[ASN][1000 genomes]
rs1097068	0.81[ASN][1000 genomes]
rs1097070	0.81[ASN][1000 genomes]
rs1103115	0.84[ASN][1000 genomes]
rs11205354	0.81[AMR][1000 genomes]
rs11205357	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs11205359	0.92[ASN][1000 genomes]
rs11205373	0.87[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs1122967	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1145583	0.84[ASN][1000 genomes]
rs11577843	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap]
rs11581351	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap]
rs11587575	0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11587758	0.84[ASN][1000 genomes]
rs12029359	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs12040949	0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs12046899	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs12057558	1.00[YRI][hapmap]
rs1260367	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1260368	0.84[ASN][1000 genomes]
rs1260396	0.92[ASN][1000 genomes]
rs1260398	0.92[ASN][1000 genomes]
rs1260400	0.83[ASN][1000 genomes]
rs1260404	0.85[ASN][1000 genomes]
rs1260405	0.84[ASN][1000 genomes]
rs1260406	0.84[ASN][1000 genomes]
rs1260407	0.93[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1260409	0.83[ASN][1000 genomes]
rs1260411	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1260458	0.84[ASN][1000 genomes]
rs1260459	0.82[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs12747669	0.81[ASN][1000 genomes]
rs1313570	0.84[ASN][1000 genomes]
rs1498308	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1614039	0.87[ASN][1000 genomes]
rs1625468	0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs1694364	0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1694369	0.84[ASN][1000 genomes]
rs1694370	0.91[ASN][1000 genomes]
rs1694375	0.89[ASN][1000 genomes]
rs1694377	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs1694380	0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1694381	0.89[ASN][1000 genomes]
rs1747927	0.88[ASN][1000 genomes]
rs17596326	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1776273	0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs1776274	0.94[ASN][1000 genomes]
rs1776276	0.86[ASN][1000 genomes]
rs1932934	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2147324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318761	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2454285	0.87[ASN][1000 genomes]
rs2454286	0.81[ASN][1000 genomes]
rs2477121	0.80[ASN][1000 genomes]
rs2762860	0.90[ASN][1000 genomes]
rs2794615	0.80[ASN][1000 genomes]
rs2794678	0.84[ASN][1000 genomes]
rs2794679	0.82[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2794681	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2794682	0.82[ASN][1000 genomes]
rs2794684	0.83[ASN][1000 genomes]
rs2794685	0.84[ASN][1000 genomes]
rs2797653	0.84[ASN][1000 genomes]
rs2873669	0.81[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs3125808	0.85[ASN][1000 genomes]
rs4333886	0.88[ASN][1000 genomes]
rs4581308	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs471464	0.91[ASN][1000 genomes]
rs471738	0.93[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs486275	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs488271	0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4926394	0.80[ASN][1000 genomes]
rs4926395	0.87[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4926419	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4926422	0.85[ASN][1000 genomes]
rs494952	0.81[ASN][1000 genomes]
rs497128	0.85[ASN][1000 genomes]
rs500812	0.88[ASN][1000 genomes]
rs509345	0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs519126	0.87[ASN][1000 genomes]
rs521607	0.90[ASN][1000 genomes]
rs522435	0.85[ASN][1000 genomes]
rs543179	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs56214461	0.88[ASN][1000 genomes]
rs573351	0.80[ASN][1000 genomes]
rs578353	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs580060	0.92[ASN][1000 genomes]
rs580159	0.92[ASN][1000 genomes]
rs6662108	0.81[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs6676685	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6685252	0.96[ASN][1000 genomes]
rs696616	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs696618	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs698913	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs698916	0.81[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs698918	0.84[ASN][1000 genomes]
rs7002	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7511649	0.93[CHB][hapmap];1.00[YRI][hapmap]
rs7512552	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7517441	0.93[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7523428	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs7548085	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs7554686	0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs8006	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs832621	0.80[ASN][1000 genomes]
rs832622	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap]
rs834231	0.81[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs834232	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs834234	0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs834241	0.80[ASN][1000 genomes]
rs834242	0.87[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs834243	0.82[ASN][1000 genomes]
rs9435997	0.88[ASN][1000 genomes]
rs9436112	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150241800-150253400	Weak transcription	Ovary	ovary
2	chr1:150241800-150253800	Weak transcription	Esophagus	oesophagus
3	chr1:150241800-150253800	Weak transcription	Gastric	stomach
4	chr1:150241800-150254200	Weak transcription	Spleen	Spleen
5	chr1:150242000-150253400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:150242000-150253800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:150242200-150253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:150242200-150253200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:150242200-150253400	Weak transcription	Primary T cells from cord blood	blood
10	chr1:150242200-150253400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:150242400-150253000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:150242400-150253200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:150242600-150253200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:150245400-150253600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:150245600-150253200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:150245600-150253400	Weak transcription	Placenta	Placenta
17	chr1:150245600-150253800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:150245600-150253800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:150245600-150253800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:150245600-150253800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:150245600-150254200	Weak transcription	Lung	lung
22	chr1:150245800-150253400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:150245800-150253800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:150245800-150253800	Weak transcription	Left Ventricle	heart
25	chr1:150245800-150253800	Weak transcription	Right Ventricle	heart
26	chr1:150245800-150254000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:150246000-150253400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:150246000-150253400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:150246000-150253800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:150246000-150254000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:150246200-150253400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:150246200-150253400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:150246200-150253400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:150246200-150253600	Weak transcription	Fetal Kidney	kidney
35	chr1:150246200-150254000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:150246400-150253000	Weak transcription	NHLF	lung
37	chr1:150246400-150253400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:150246600-150253000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:150246600-150253000	Weak transcription	Fetal Lung	lung
40	chr1:150246600-150253200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:150246600-150253400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:150246600-150253400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:150246600-150253400	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:150246600-150253800	Weak transcription	HUVEC	blood vessel
45	chr1:150246800-150253000	Weak transcription	NH-A	brain
46	chr1:150246800-150253400	Weak transcription	Brain Substantia Nigra	brain
47	chr1:150247400-150253800	Weak transcription	K562	blood
48	chr1:150248400-150253600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:150249200-150253400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:150249200-150253400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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