Variant report

Variant	rs6747792
Chromosome Location	chr2:148611528-148611529
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:148600808..148604686-chr2:148606929..148611587,8	K562	blood:
2	chr2:148606424..148608489-chr2:148610392..148613809,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121989	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1234398	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1234414	0.87[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1234417	1.00[YRI][hapmap]
rs1406444	0.94[CHD][hapmap];0.81[JPT][hapmap]
rs1424941	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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469211	0.82[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17218938	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17225402	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17225423	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17225430	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17232078	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17691284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17692648	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17741344	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17741978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17742134	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17742246	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17742342	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17743157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1994189	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs3754541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820715	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62169472	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169473	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169474	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169475	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62169477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169478	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169479	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs730356	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7560502	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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7595052	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602296	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs929940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs981814	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6747792	LYPD6	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148604000-148612600	Weak transcription	Gastric	stomach
2	chr2:148604000-148620000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:148604600-148612400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:148604600-148612400	Weak transcription	Left Ventricle	heart
5	chr2:148604600-148612400	Weak transcription	Right Ventricle	heart
6	chr2:148604600-148612600	Weak transcription	Pancreas	Pancrea
7	chr2:148604600-148614600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:148604600-148616400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:148604600-148617200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:148604600-148617600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:148604600-148617600	Weak transcription	HSMM	muscle
12	chr2:148604800-148612800	Weak transcription	Right Atrium	heart
13	chr2:148605600-148612800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:148605600-148613200	Enhancers	HepG2	liver
15	chr2:148605600-148614600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:148606000-148612200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:148606000-148614200	Weak transcription	Brain Germinal Matrix	brain
18	chr2:148606000-148614600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:148606000-148620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:148606000-148627600	Weak transcription	Brain Angular Gyrus	brain
21	chr2:148606200-148620800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:148607400-148617400	Weak transcription	Fetal Brain Female	brain
23	chr2:148607800-148615600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:148608000-148612600	Weak transcription	Psoas Muscle	Psoas
25	chr2:148608000-148612600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:148608000-148612800	Weak transcription	Fetal Brain Male	brain
27	chr2:148608200-148614800	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:148608600-148612800	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:148608600-148616800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:148608800-148612400	Weak transcription	Small Intestine	intestine
31	chr2:148608800-148617400	Weak transcription	HSMMtube	muscle
32	chr2:148609000-148617000	Weak transcription	Adipose Nuclei	Adipose
33	chr2:148609200-148612200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:148609200-148612600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:148609200-148614400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:148609400-148611600	Weak transcription	Stomach Mucosa	stomach
37	chr2:148609400-148612200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:148609400-148616000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:148609400-148619600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:148609400-148620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:148609600-148611600	Weak transcription	Liver	Liver
42	chr2:148610200-148613000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:148610400-148616200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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