Variant report

Variant	rs56017742
Chromosome Location	chr13:51970505-51970506
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51968496..51970934-chr13:52376792..52378777,2	K562	blood:
2	chr13:51970484..51973482-chr13:52022310..52025240,2	K562	blood:
3	chr13:51967878..51970855-chr13:52024564..52027900,3	K562	blood:
4	chr13:51966813..51968638-chr13:51968842..51971836,2	K562	blood:
5	chr13:51970051..51972806-chr13:52025800..52028354,2	MCF-7	breast:
6	chr13:51970413..51974561-chr13:52025794..52028654,4	K562	blood:
7	chr13:51970247..51972973-chr13:51973755..51976105,2	K562	blood:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000231856	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1028727	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17194948	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17195020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2026526	0.84[ASN][1000 genomes]
rs2408363	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4628860	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73197809	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73197821	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73197824	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7328715	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7335122	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7335144	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7337450	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7989850	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9316541	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316545	0.84[ASN][1000 genomes]
rs9316546	0.84[ASN][1000 genomes]
rs9526757	0.95[EUR][1000 genomes]
rs9526758	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526759	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526761	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526764	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535640	0.85[EUR][1000 genomes]
rs9535644	0.81[EUR][1000 genomes]
rs9535646	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535652	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535655	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535660	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535661	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535662	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535663	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535665	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535670	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535671	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535678	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535680	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535682	0.92[ASN][1000 genomes]
rs9535683	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535689	0.82[ASN][1000 genomes]
rs9535694	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9535699	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9563046	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9634842	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56017742	INTS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51935600-51971400	Weak transcription	Gastric	stomach
2	chr13:51939200-51970600	Weak transcription	Brain Angular Gyrus	brain
3	chr13:51945200-51970600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:51945200-51971600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:51945400-51970600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr13:51945800-52016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr13:51946200-51988000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:51946400-51971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr13:51947000-51970800	Weak transcription	Brain Hippocampus Middle	brain
10	chr13:51948000-51970800	Weak transcription	A549	lung
11	chr13:51948000-51971400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:51948600-51971600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:51948600-51971600	Weak transcription	Small Intestine	intestine
14	chr13:51949000-51971400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr13:51949400-51971400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:51949400-51971400	Weak transcription	Esophagus	oesophagus
17	chr13:51949400-51971400	Weak transcription	Pancreas	Pancrea
18	chr13:51949400-52025000	Weak transcription	Fetal Muscle Leg	muscle
19	chr13:51950000-51970600	Weak transcription	Brain Substantia Nigra	brain
20	chr13:51950000-51971400	Weak transcription	Fetal Stomach	stomach
21	chr13:51950000-51971400	Weak transcription	Left Ventricle	heart
22	chr13:51950000-51971800	Weak transcription	Lung	lung
23	chr13:51950000-52025200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr13:51950200-51999800	Weak transcription	Brain Germinal Matrix	brain
25	chr13:51951800-51970600	Weak transcription	Hela-S3	cervix
26	chr13:51952400-51970600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr13:51952400-51971400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr13:51952600-51970800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr13:51952600-51970800	Weak transcription	HSMMtube	muscle
30	chr13:51952600-51971400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr13:51953200-51970600	Weak transcription	Colon Smooth Muscle	Colon
32	chr13:51954000-51970600	Weak transcription	K562	blood
33	chr13:51955200-51973600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:51957200-51971400	Weak transcription	Fetal Intestine Small	intestine
35	chr13:51957400-51978200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr13:51957800-51971600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr13:51957800-51978400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:51957800-51986600	Weak transcription	Fetal Thymus	thymus
39	chr13:51958000-51970600	Weak transcription	Adipose Nuclei	Adipose
40	chr13:51958000-51970800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr13:51958000-51970800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:51958000-51971400	Weak transcription	Fetal Lung	lung
43	chr13:51958000-51971600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr13:51958000-51971600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr13:51958000-51996800	Weak transcription	Thymus	Thymus
46	chr13:51958200-51971400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:51958200-51990000	Weak transcription	HMEC	breast
48	chr13:51958400-51987800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr13:51959200-51981200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr13:51959400-51971400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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