Variant report

Variant	rs1117490
Chromosome Location	chr6:30170510-30170511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30170480..30172183-chr6:30179572..30182073,2	MCF-7	breast:
2	chr6:30164991..30167307-chr6:30168742..30170547,2	K562	blood:
3	chr6:30168637..30170794-chr6:30170971..30172497,2	K562	blood:
4	chr6:30164724..30168214-chr6:30169655..30171651,4	MCF-7	breast:
5	chr6:30164021..30166889-chr6:30166891..30170637,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1117487	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117488	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969573	0.81[ASN][1000 genomes]
rs2021722	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023475	0.81[ASN][1000 genomes]
rs2284166	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428503	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2517590	0.81[ASN][1000 genomes]
rs2517608	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517611	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2517614	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2523713	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523714	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523716	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2523721	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2523722	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28360014	0.81[ASN][1000 genomes]
rs2844776	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132672	0.80[AFR][1000 genomes]
rs55957413	0.81[ASN][1000 genomes]
rs59975149	0.81[ASN][1000 genomes]
rs61154150	0.81[ASN][1000 genomes]
rs885912	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971570	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1117490	ZKSCAN3	cis	parietal	SCAN
rs1117490	BTN2A1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30145000-30173800	Weak transcription	Right Atrium	heart
2	chr6:30148000-30173000	Weak transcription	Fetal Heart	heart
3	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:30152000-30170600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:30152000-30172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:30156800-30174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:30157000-30171800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:30158200-30173600	Weak transcription	Psoas Muscle	Psoas
9	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
10	chr6:30162600-30170600	Strong transcription	Dnd41	blood
11	chr6:30162800-30170600	Strong transcription	Fetal Thymus	thymus
12	chr6:30163800-30170600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:30167000-30173000	Weak transcription	Brain Germinal Matrix	brain
14	chr6:30167000-30178000	Weak transcription	Fetal Brain Female	brain
15	chr6:30168200-30171200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr6:30168400-30170600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
17	chr6:30168400-30174000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:30168600-30171200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:30168600-30171600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:30168600-30171800	Weak transcription	Lung	lung
21	chr6:30168600-30172800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:30168600-30174000	Weak transcription	NH-A	brain
23	chr6:30168600-30174000	Weak transcription	NHLF	lung
24	chr6:30168800-30170600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:30168800-30170800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:30168800-30170800	Enhancers	Duodenum Mucosa	Duodenum
27	chr6:30168800-30171400	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:30168800-30171600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:30168800-30171600	Weak transcription	Brain Substantia Nigra	brain
30	chr6:30168800-30171800	Weak transcription	Brain Angular Gyrus	brain
31	chr6:30168800-30173400	Weak transcription	Gastric	stomach
32	chr6:30168800-30174800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:30168800-30179800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:30169000-30171400	Weak transcription	HMEC	breast
35	chr6:30169000-30171600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:30169000-30171600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:30169000-30171800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:30169000-30171800	Weak transcription	Brain Anterior Caudate	brain
39	chr6:30169000-30171800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:30169000-30171800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:30169000-30171800	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:30169000-30171800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:30169000-30172600	Weak transcription	Esophagus	oesophagus
44	chr6:30169000-30173000	Weak transcription	Thymus	Thymus
45	chr6:30169000-30173200	Weak transcription	Pancreas	Pancrea
46	chr6:30169000-30173400	Weak transcription	Left Ventricle	heart
47	chr6:30169000-30173800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:30169000-30173800	Weak transcription	NHDF-Ad	bronchial
49	chr6:30169000-30174000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:30169000-30174000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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