Variant report

Variant	rs6689338
Chromosome Location	chr1:150255658-150255659
allele	A/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	MXI1	chr1:150253414-150255748	IMR90	lung:	n/a	n/a
2	MAZ	chr1:150253610-150255847	IMR90	lung:	n/a	chr1:150254466-150254475 chr1:150255121-150255132 chr1:150254829-150254848 chr1:150254467-150254474 chr1:150254834-150254843 chr1:150255120-150255133 chr1:150255122-150255131 chr1:150254468-150254484 chr1:150254836-150254843
3	SIN3AK20	chr1:150253386-150255703	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150226594..150229990-chr1:150253466..150255722,4	K562	blood:
2	chr1:144532574..144534383-chr1:150253333..150256090,2	K562	blood:
3	chr1:150254809..150257635-chr11:62608044..62609557,2	MCF-7	breast:
4	chr1:150254416..150258326-chr1:150293142..150296194,3	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	chr1:150252171..150257673-chr1:150291650..150295636,15	MCF-7	breast:
8	chr1:150254103..150255766-chr1:150487973..150490880,2	MCF-7	breast:
9	chr1:150254313..150256354-chr20:49126871..49128385,2	MCF-7	breast:
10	chr1:150253619..150256471-chr1:150290811..150295516,7	MCF-7	breast:
11	chr1:150205879..150210456-chr1:150251557..150256195,8	MCF-7	breast:
12	chr1:150232148..150235043-chr1:150254020..150257209,3	K562	blood:

Variant related genes	Relation type
C1orf51	TF binding region
ENSG00000228126	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000196396	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000118298	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000238526	Chromatin interaction
ENSG00000271845	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000143401	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10158314	1.00[EUR][1000 genomes]
rs10494265	1.00[EUR][1000 genomes]
rs10788868	1.00[EUR][1000 genomes]
rs12749958	0.82[AFR][1000 genomes]
rs13374103	1.00[EUR][1000 genomes]
rs13375753	1.00[EUR][1000 genomes]
rs1545761	1.00[EUR][1000 genomes]
rs16833591	1.00[EUR][1000 genomes]
rs16835652	1.00[EUR][1000 genomes]
rs3118123	1.00[EUR][1000 genomes]
rs4845	1.00[YRI][hapmap]
rs56877951	1.00[EUR][1000 genomes]
rs57788184	1.00[EUR][1000 genomes]
rs57819791	1.00[EUR][1000 genomes]
rs58922427	1.00[EUR][1000 genomes]
rs59082627	1.00[EUR][1000 genomes]
rs59682561	1.00[EUR][1000 genomes]
rs59821426	1.00[EUR][1000 genomes]
rs60109648	1.00[EUR][1000 genomes]
rs60307722	1.00[EUR][1000 genomes]
rs60616215	1.00[EUR][1000 genomes]
rs6587748	1.00[EUR][1000 genomes]
rs6671747	1.00[EUR][1000 genomes]
rs6680474	1.00[EUR][1000 genomes]
rs6689495	1.00[EUR][1000 genomes]
rs71622689	0.82[AFR][1000 genomes]
rs73011246	1.00[EUR][1000 genomes]
rs73011248	1.00[EUR][1000 genomes]
rs73011264	1.00[EUR][1000 genomes]
rs73011271	1.00[EUR][1000 genomes]
rs73011273	1.00[EUR][1000 genomes]
rs73011380	1.00[EUR][1000 genomes]
rs73016142	1.00[EUR][1000 genomes]
rs73016148	1.00[EUR][1000 genomes]
rs74124337	1.00[EUR][1000 genomes]
rs74124339	1.00[EUR][1000 genomes]
rs7517003	0.82[AFR][1000 genomes]
rs7520088	1.00[EUR][1000 genomes]
rs7527755	1.00[EUR][1000 genomes]
rs7548450	1.00[EUR][1000 genomes]
rs946521	1.00[EUR][1000 genomes]

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:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150253400-150256000	Active TSS	Right Atrium	heart
2	chr1:150253400-150256000	Flanking Active TSS	HMEC	breast
3	chr1:150253600-150255800	Active TSS	Brain Angular Gyrus	brain
4	chr1:150253600-150256200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:150253600-150256200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:150253800-150255800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:150253800-150255800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:150253800-150255800	Flanking Active TSS	Fetal Intestine Large	intestine
9	chr1:150253800-150255800	Active TSS	Right Ventricle	heart
10	chr1:150253800-150256000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr1:150253800-150256000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:150253800-150256000	Active TSS	Brain Substantia Nigra	brain
13	chr1:150254000-150256000	Active TSS	Rectal Smooth Muscle	rectum
14	chr1:150254200-150255800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:150254200-150255800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
16	chr1:150254400-150256000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:150254400-150260600	Weak transcription	K562	blood
18	chr1:150254600-150255800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:150254600-150256000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:150254600-150256000	Active TSS	HSMM	muscle
21	chr1:150254600-150266200	Weak transcription	Small Intestine	intestine
22	chr1:150255000-150255800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:150255000-150255800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr1:150255000-150256000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:150255000-150256000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:150255000-150256000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr1:150255000-150256200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:150255000-150256200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr1:150255000-150256200	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr1:150255200-150255800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:150255200-150255800	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:150255200-150256200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:150255200-150256200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:150255400-150255800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr1:150255400-150255800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:150255400-150255800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:150255400-150255800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:150255400-150255800	Active TSS	Duodenum Mucosa	Duodenum
39	chr1:150255400-150255800	Flanking Active TSS	Fetal Brain Male	brain
40	chr1:150255400-150255800	Bivalent Enhancer	Fetal Thymus	thymus
41	chr1:150255400-150255800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:150255400-150255800	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:150255400-150256000	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr1:150255400-150256000	Active TSS	Colonic Mucosa	Colon
45	chr1:150255400-150256000	Enhancers	Esophagus	oesophagus
46	chr1:150255400-150256000	Flanking Active TSS	Fetal Brain Female	brain
47	chr1:150255400-150256000	Enhancers	Fetal Lung	lung
48	chr1:150255400-150256000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr1:150255400-150256000	Flanking Active TSS	NHEK	skin
50	chr1:150255400-150256200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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