Variant report

Variant	rs162139
Chromosome Location	chr5:98199423-98199424
allele	C/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	POLR2A	chr5:98199054-98200787	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98196576..98199653-chr5:98202871..98206986,3	K562	blood:

Variant related genes	Relation type
CHD1	TF binding region
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10044680	1.00[EUR][1000 genomes]
rs10045317	0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10046011	1.00[EUR][1000 genomes]
rs10060286	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13358830	1.00[EUR][1000 genomes]
rs1382336	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs161743	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs162141	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs162142	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162143	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162146	1.00[AMR][1000 genomes]
rs162157	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs162160	1.00[EUR][1000 genomes]
rs162161	0.80[AFR][1000 genomes]
rs162162	0.84[ASW][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs170579	1.00[EUR][1000 genomes]
rs17166397	1.00[EUR][1000 genomes]
rs17166450	1.00[EUR][1000 genomes]
rs17166454	0.85[LWK][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs179175	1.00[EUR][1000 genomes]
rs1828171	0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28782775	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs325193	1.00[AMR][1000 genomes]
rs325198	1.00[EUR][1000 genomes]
rs325210	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs325216	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs327801	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs327802	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs327805	1.00[EUR][1000 genomes]
rs451883	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57969582	1.00[EUR][1000 genomes]
rs59156696	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61578983	1.00[EUR][1000 genomes]
rs6891520	1.00[EUR][1000 genomes]
rs73151499	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73153514	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73153532	1.00[EUR][1000 genomes]
rs73155421	1.00[EUR][1000 genomes]
rs73155423	1.00[EUR][1000 genomes]
rs734124	1.00[AMR][1000 genomes]
rs7727696	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98180200-98213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:98182400-98203600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:98182600-98205000	Weak transcription	NHEK	skin
4	chr5:98183000-98201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:98185200-98203400	Weak transcription	Pancreas	Pancrea
6	chr5:98186200-98213400	Weak transcription	Esophagus	oesophagus
7	chr5:98186400-98200800	Weak transcription	Psoas Muscle	Psoas
8	chr5:98188400-98247000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:98189200-98205000	Weak transcription	NHLF	lung
10	chr5:98189400-98200000	Weak transcription	Left Ventricle	heart
11	chr5:98189400-98205800	Weak transcription	Fetal Heart	heart
12	chr5:98189400-98227400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:98189600-98213800	Weak transcription	HSMMtube	muscle
14	chr5:98189600-98215400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:98189600-98241000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:98189800-98241000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:98189800-98241400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:98189800-98241400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:98189800-98241800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:98190000-98203400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:98190000-98240600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr5:98190000-98240800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr5:98190000-98240800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:98190200-98203600	Weak transcription	Right Ventricle	heart
25	chr5:98190200-98204200	Weak transcription	Brain Substantia Nigra	brain
26	chr5:98190200-98240600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:98190200-98240600	Strong transcription	Liver	Liver
28	chr5:98190200-98241000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr5:98190400-98199800	Weak transcription	Colonic Mucosa	Colon
30	chr5:98190400-98200200	Weak transcription	Lung	lung
31	chr5:98190400-98200800	Weak transcription	Fetal Brain Female	brain
32	chr5:98190400-98203400	Weak transcription	Spleen	Spleen
33	chr5:98190400-98203600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:98190400-98203600	Weak transcription	Gastric	stomach
35	chr5:98190400-98205400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:98190400-98212400	Weak transcription	Small Intestine	intestine
37	chr5:98190400-98213200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:98190400-98214600	Weak transcription	Aorta	Aorta
39	chr5:98190400-98224200	Strong transcription	Placenta	Placenta
40	chr5:98190400-98234600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:98190400-98238200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:98190400-98238800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:98190400-98240000	Weak transcription	Stomach Mucosa	stomach
44	chr5:98190400-98240400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:98190400-98240600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr5:98190400-98240800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr5:98190400-98241200	Strong transcription	Fetal Thymus	thymus
48	chr5:98190400-98243800	Strong transcription	Dnd41	blood
49	chr5:98190600-98209400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:98190600-98240600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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