Variant report

Variant	rs35345226
Chromosome Location	chr6:28091580-28091581
allele	A/G
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	chr6:28091409-28092994	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:27858930..27860939-chr6:28090408..28092869,2	MCF-7	breast:
2	chr6:27860877..27862510-chr6:28089122..28091622,2	K562	blood:
3	chr6:28091137..28098786-chr6:28103559..28111884,14	MCF-7	breast:
4	chr6:27803895..27805819-chr6:28090155..28092205,2	MCF-7	breast:
5	chr6:28083288..28085321-chr6:28091167..28093208,2	MCF-7	breast:

Variant related genes	Relation type
ZSCAN16	TF binding region
ENSG00000196331	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000219392	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000269293	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs13190888	0.81[EUR][1000 genomes]
rs13191786	0.85[EUR][1000 genomes]
rs13195291	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13197176	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13197574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13197633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13198809	0.85[EUR][1000 genomes]
rs13200214	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13201308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13204012	0.85[EUR][1000 genomes]
rs13205211	0.85[EUR][1000 genomes]
rs13205911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13207345	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13208096	0.85[EUR][1000 genomes]
rs13211507	0.85[EUR][1000 genomes]
rs13217619	1.00[AFR][1000 genomes]
rs13217984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33932084	0.84[EUR][1000 genomes]
rs34166054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34218844	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34243448	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34371502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34396849	0.85[EUR][1000 genomes]
rs34505829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34588114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34661125	0.85[EUR][1000 genomes]
rs34662244	0.82[EUR][1000 genomes]
rs34691223	0.85[EUR][1000 genomes]
rs34765154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34832585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34878803	0.85[EUR][1000 genomes]
rs34950484	0.85[EUR][1000 genomes]
rs35001169	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35016036	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35030260	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35072899	0.85[EUR][1000 genomes]
rs35098436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35353359	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35656932	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35744819	0.85[EUR][1000 genomes]
rs35749575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35781323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35902873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35952432	0.90[EUR][1000 genomes]
rs56075693	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56189111	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs66886492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67297533	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67340775	0.84[EUR][1000 genomes]
rs67998226	0.85[EUR][1000 genomes]
rs68188794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71537572	1.00[AFR][1000 genomes]
rs71559070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71559072	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72846780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72846794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72854513	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35345226	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs35345226	AL022393.7	cis	Muscle Skeletal	GTEx
rs35345226	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs35345226	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28073200-28091800	Weak transcription	Right Ventricle	heart
2	chr6:28073400-28091800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:28073400-28091800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:28073400-28091800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:28073400-28092000	Weak transcription	Small Intestine	intestine
6	chr6:28073400-28092200	Weak transcription	Esophagus	oesophagus
7	chr6:28073400-28092200	Weak transcription	Gastric	stomach
8	chr6:28073400-28092200	Weak transcription	Pancreas	Pancrea
9	chr6:28073600-28091600	Weak transcription	Hela-S3	cervix
10	chr6:28073600-28091600	Weak transcription	NHEK	skin
11	chr6:28077000-28092400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28080000-28092000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:28080400-28091600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:28080800-28092000	Weak transcription	Fetal Intestine Small	intestine
15	chr6:28081200-28091600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:28081200-28091800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:28081400-28091600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:28081400-28091800	Weak transcription	Colonic Mucosa	Colon
19	chr6:28081600-28091800	Weak transcription	HMEC	breast
20	chr6:28082000-28091600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:28082000-28092200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:28082600-28091600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:28082600-28096200	Strong transcription	Dnd41	blood
24	chr6:28084000-28091600	Weak transcription	Fetal Heart	heart
25	chr6:28084200-28091600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:28084200-28091800	Weak transcription	Psoas Muscle	Psoas
27	chr6:28084200-28091800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:28084200-28092200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:28084400-28091600	Weak transcription	Fetal Kidney	kidney
30	chr6:28084400-28091800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:28084400-28092000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:28084400-28092000	Weak transcription	Aorta	Aorta
33	chr6:28084600-28091600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:28084600-28092200	Weak transcription	Lung	lung
35	chr6:28084600-28092200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:28084800-28091600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:28084800-28091800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:28084800-28091800	Weak transcription	Brain Substantia Nigra	brain
39	chr6:28084800-28091800	Weak transcription	HUVEC	blood vessel
40	chr6:28084800-28092200	Weak transcription	Spleen	Spleen
41	chr6:28086400-28091800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:28086600-28091600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:28086600-28091600	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:28086600-28091600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:28086600-28091600	Weak transcription	GM12878-XiMat	blood
46	chr6:28086600-28091800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:28086600-28091800	Weak transcription	A549	lung
48	chr6:28086800-28091600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:28086800-28091600	Weak transcription	Brain Anterior Caudate	brain
50	chr6:28087200-28091800	Weak transcription	HSMMtube	muscle

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