Variant report

Variant	rs3757188
Chromosome Location	chr6:28107357-28107358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
2	chr6:28107272..28109222-chr6:28196565..28198817,2	K562	blood:
3	chr6:27857129..27859629-chr6:28105020..28108475,3	K562	blood:
4	chr6:27802664..27806163-chr6:28103303..28107418,3	K562	blood:
5	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
6	chr6:28106928..28109553-chr6:28206567..28208256,2	MCF-7	breast:
7	chr6:28106686..28108763-chr6:28154125..28157029,2	K562	blood:
8	chr6:28105533..28107833-chr6:28443278..28445327,2	MCF-7	breast:
9	chr6:28107051..28109226-chr6:28248173..28249802,2	K562	blood:
10	chr6:28091137..28098786-chr6:28103559..28111884,14	MCF-7	breast:
11	chr6:28107051..28109569-chr6:28248173..28249802,3	K562	blood:
12	chr6:28107084..28109102-chr6:28365969..28368656,2	K562	blood:
13	chr6:28106596..28109035-chr6:28311794..28313364,2	K562	blood:
14	chr6:28099723..28110178-chr6:28301599..28306918,14	K562	blood:
15	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF192-1	chr6:28104627-28107456	ENSG00000261839.1

No data

Variant related genes	Relation type
ENSG00000184348	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196812	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000218016	Chromatin interaction
ENSG00000176933	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10456362	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs11965538	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs12055625	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs13200462	0.93[CEU][hapmap]
rs1321504	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1321505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437126	1.00[ASN][1000 genomes]
rs13437444	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1419183	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs149943	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs149990	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs1679709	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs1679732	0.93[CEU][hapmap]
rs16893573	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs16893601	1.00[CHB][hapmap]
rs16893735	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17720293	0.85[CEU][hapmap]
rs1778507	0.81[GIH][hapmap];0.90[YRI][hapmap]
rs1778508	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs1778511	0.93[CEU][hapmap]
rs202906	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2799077	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs2799079	0.93[CEU][hapmap]
rs34130214	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712084	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs4713138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4713139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901575	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs6920512	0.90[YRI][hapmap]
rs735765	0.93[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180562	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs904142	0.90[CHD][hapmap]
rs9295765	1.00[YRI][hapmap]
rs9348792	0.94[ASN][1000 genomes]
rs9357064	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9366717	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs9368560	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9368561	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380030	0.90[CHD][hapmap]
rs9380031	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs9380032	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9380051	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9380064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380069	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs9393882	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9393889	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9393902	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9393908	0.80[CEU][hapmap];0.92[EUR][1000 genomes]
rs9461432	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461439	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9461446	0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9468287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468300	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468301	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9468321	1.00[YRI][hapmap]
rs9468322	0.81[GIH][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9468342	1.00[YRI][hapmap]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3757188	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3757188	ZNF192	cis	cerebellum	SCAN
rs3757188	VCAN	trans	lymphoblastoid	seeQTL
rs3757188	AL022393.7	cis	Muscle Skeletal	GTEx
rs3757188	LRRC16A	cis	parietal	SCAN
rs3757188	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs3757188	RP5-874C20.3	cis	Thyroid	GTEx
rs3757188	ZNF323	cis	parietal	SCAN
rs3757188	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3757188	ZSCAN23	cis	cerebellum	SCAN
rs3757188	BTN3A2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28105600-28109200	Weak transcription	Gastric	stomach
2	chr6:28105800-28107800	Weak transcription	Ovary	ovary
3	chr6:28105800-28107800	Weak transcription	Right Atrium	heart
4	chr6:28105800-28108800	Weak transcription	Stomach Mucosa	stomach
5	chr6:28105800-28109000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:28105800-28109000	Weak transcription	Placenta	Placenta
7	chr6:28105800-28109000	Weak transcription	A549	lung
8	chr6:28105800-28109200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:28105800-28109200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:28105800-28109200	Weak transcription	Esophagus	oesophagus
11	chr6:28105800-28109200	Weak transcription	Left Ventricle	heart
12	chr6:28105800-28109200	Weak transcription	Lung	lung
13	chr6:28105800-28109200	Weak transcription	Pancreas	Pancrea
14	chr6:28106000-28107800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:28106000-28107800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:28106000-28107800	Weak transcription	Liver	Liver
17	chr6:28106000-28107800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:28106000-28108000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr6:28106000-28108000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:28106000-28108000	Weak transcription	Osteobl	bone
21	chr6:28106000-28108200	Weak transcription	NHDF-Ad	bronchial
22	chr6:28106000-28108800	Weak transcription	NHLF	lung
23	chr6:28106000-28109000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:28106000-28109000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:28106000-28109000	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:28106000-28109000	Weak transcription	HSMMtube	muscle
27	chr6:28106000-28109000	Weak transcription	NH-A	brain
28	chr6:28106000-28109200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:28106000-28109200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:28106000-28109200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:28106000-28109200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:28106000-28109200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:28106000-28109200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:28106000-28109200	Weak transcription	Brain Angular Gyrus	brain
35	chr6:28106000-28109200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:28106000-28109200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:28106000-28109200	Weak transcription	Colonic Mucosa	Colon
38	chr6:28106000-28109200	Weak transcription	Fetal Brain Male	brain
39	chr6:28106000-28109200	Weak transcription	Fetal Intestine Large	intestine
40	chr6:28106000-28109200	Weak transcription	Fetal Kidney	kidney
41	chr6:28106000-28109200	Weak transcription	Right Ventricle	heart
42	chr6:28106000-28109200	Weak transcription	Small Intestine	intestine
43	chr6:28106000-28109200	Weak transcription	Spleen	Spleen
44	chr6:28106000-28109200	Weak transcription	HMEC	breast
45	chr6:28106000-28109200	Weak transcription	HSMM	muscle
46	chr6:28106000-28109200	Weak transcription	NHEK	skin
47	chr6:28106200-28107600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:28106200-28107600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:28106200-28107600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:28106200-28107600	Weak transcription	Duodenum Mucosa	Duodenum

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