Variant report

Variant	rs6659285
Chromosome Location	chr1:78139812-78139813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78129208..78133797-chr1:78137082..78139912,5	K562	blood:
2	chr1:78139754..78141838-chr1:78469324..78471683,2	K562	blood:
3	chr1:78134917..78136892-chr1:78138140..78140290,2	MCF-7	breast:
4	chr1:78137920..78140164-chr1:78468661..78471573,4	K562	blood:

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs17100817	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17100819	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1874816	1.00[CEU][hapmap]
rs34351666	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34974859	0.93[EUR][1000 genomes]
rs41313399	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6603957	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6604877	1.00[CEU][hapmap]
rs6660964	1.00[CEU][hapmap]
rs6662245	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6666107	0.80[EUR][1000 genomes]
rs6677011	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6678173	0.87[EUR][1000 genomes]
rs6679645	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6701361	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7523258	1.00[CEU][hapmap]
rs7525538	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7532455	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7546155	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7546605	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7550587	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7555421	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7555864	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9659817	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
7	esv1796958	chr1:78138955-78267421	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78099000-78147200	Weak transcription	Gastric	stomach
2	chr1:78107600-78146000	Weak transcription	Fetal Kidney	kidney
3	chr1:78111200-78147200	Weak transcription	Esophagus	oesophagus
4	chr1:78116800-78144600	Weak transcription	NHEK	skin
5	chr1:78117200-78144400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:78117400-78141800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:78117400-78147200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:78117600-78146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:78117600-78147200	Weak transcription	Thymus	Thymus
10	chr1:78118600-78146000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:78119000-78145600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:78119000-78146000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:78119400-78147200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:78120800-78147200	Weak transcription	Lung	lung
15	chr1:78124600-78146000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:78127000-78146400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:78128800-78141000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:78128800-78141800	Weak transcription	Fetal Intestine Small	intestine
19	chr1:78131000-78141800	Weak transcription	Fetal Stomach	stomach
20	chr1:78131000-78146800	Weak transcription	Fetal Brain Female	brain
21	chr1:78131800-78145000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:78132000-78144200	Weak transcription	Adipose Nuclei	Adipose
23	chr1:78132000-78147200	Weak transcription	Right Ventricle	heart
24	chr1:78132200-78141800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:78133800-78143600	Weak transcription	Fetal Intestine Large	intestine
26	chr1:78135000-78146800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:78135200-78141000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:78136400-78147200	Weak transcription	Spleen	Spleen
29	chr1:78136800-78147200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:78137000-78140200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:78137400-78143600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:78137600-78145000	Weak transcription	Small Intestine	intestine
33	chr1:78137800-78142200	Enhancers	NHDF-Ad	bronchial
34	chr1:78137800-78146000	Weak transcription	Fetal Lung	lung
35	chr1:78137800-78146800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:78138000-78140000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:78138000-78140000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:78138000-78140200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:78138000-78141800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:78138000-78145800	Weak transcription	HMEC	breast
41	chr1:78138000-78147200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:78138200-78140000	Enhancers	Brain Angular Gyrus	brain
43	chr1:78138200-78140000	Enhancers	HSMMtube	muscle
44	chr1:78138200-78140200	Enhancers	Brain Hippocampus Middle	brain
45	chr1:78138200-78140200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr1:78138200-78140200	Enhancers	Brain Substantia Nigra	brain
47	chr1:78138200-78141600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:78138200-78141600	Enhancers	HSMM	muscle
49	chr1:78138200-78141800	Weak transcription	Fetal Thymus	thymus
50	chr1:78138200-78142200	Enhancers	Brain Anterior Caudate	brain

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