Variant report

Variant	rs3777744
Chromosome Location	chr6:35356143-35356144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35355898..35357856-chr6:35435877..35438604,2	MCF-7	breast:
2	chr6:35349215..35351614-chr6:35353846..35356843,2	MCF-7	breast:
3	chr6:35334905..35337136-chr6:35354617..35357561,2	K562	blood:
4	chr6:35343822..35346553-chr6:35354623..35356533,2	K562	blood:

Variant related genes	Relation type
ENSG00000198755	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10080411	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10755687	0.83[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10807150	0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[ASN][1000 genomes]
rs10947540	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs10947542	0.82[ASN][1000 genomes]
rs1108709	0.85[ASN][1000 genomes]
rs1194	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs12173347	0.82[ASN][1000 genomes]
rs12173582	0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs12211943	0.91[ASN][1000 genomes]
rs13214290	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs1557567	0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[ASN][1000 genomes]
rs1557568	0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[ASN][1000 genomes]
rs1888822	0.81[CHD][hapmap]
rs1888823	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs1888824	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs1888825	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs1894650	0.82[JPT][hapmap]
rs1894651	0.82[JPT][hapmap]
rs1894653	0.82[JPT][hapmap]
rs1929847	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs1929849	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs1987673	0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2032538	0.82[JPT][hapmap]
rs2071920	0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2267657	0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2267660	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs2267662	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs2267663	0.82[JPT][hapmap]
rs2267664	0.82[JPT][hapmap]
rs2284196	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395614	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2395621	0.87[ASN][1000 genomes]
rs3777742	0.85[ASN][1000 genomes]
rs3777743	0.85[ASN][1000 genomes]
rs3798342	0.82[JPT][hapmap]
rs3798343	0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs3800382	0.82[JPT][hapmap]
rs3800383	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3800385	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs3800386	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3800387	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3800388	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3800392	0.82[JPT][hapmap]
rs3800393	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4711411	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs4711413	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4713845	0.82[JPT][hapmap]
rs4713848	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs4713850	0.91[ASN][1000 genomes]
rs4713853	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713859	0.89[GIH][hapmap]
rs6457812	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6901410	0.82[ASW][hapmap]
rs6902523	0.82[JPT][hapmap]
rs6906987	0.87[ASN][1000 genomes]
rs6907364	0.89[ASN][1000 genomes]
rs6913037	0.82[JPT][hapmap]
rs6913475	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6919334	0.82[ASW][hapmap]
rs6920432	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6922548	0.82[ASW][hapmap];0.82[MKK][hapmap]
rs6930562	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6938946	0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6941471	0.87[ASN][1000 genomes]
rs7739752	0.82[ASW][hapmap]
rs7757316	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7758192	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7772302	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8205	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs914547	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs9296148	0.82[ASW][hapmap]
rs9296150	0.83[ASN][1000 genomes]
rs9366882	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9366883	0.82[JPT][hapmap]
rs9368854	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs9368857	0.82[JPT][hapmap]
rs9380500	0.82[JPT][hapmap]
rs9380501	0.82[JPT][hapmap]
rs9394288	0.82[JPT][hapmap]
rs9462065	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9469964	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs9469972	0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9469975	0.87[ASN][1000 genomes]
rs9469982	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9469997	0.91[ASN][1000 genomes]
rs9469998	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470007	0.82[ASW][hapmap];0.82[MKK][hapmap]
rs965272	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9658100	0.82[ASW][hapmap];0.82[MKK][hapmap]
rs968828	0.85[ASN][1000 genomes]
rs975496	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3777744	CPNE5	cis	parietal	SCAN
rs3777744	C6orf1	cis	parietal	SCAN
rs3777744	DEF6	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35338200-35356400	Weak transcription	Pancreas	Pancrea
2	chr6:35338400-35378400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:35338600-35359400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:35339200-35356600	Weak transcription	Esophagus	oesophagus
5	chr6:35339600-35357800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:35340000-35357600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:35340600-35359400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:35344400-35358000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:35345600-35378400	Weak transcription	Aorta	Aorta
10	chr6:35346200-35359200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:35346200-35359800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:35347400-35357600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:35347600-35359200	Weak transcription	Brain Angular Gyrus	brain
14	chr6:35347600-35359200	Weak transcription	Brain Substantia Nigra	brain
15	chr6:35349600-35359200	Weak transcription	Gastric	stomach
16	chr6:35350200-35358000	Weak transcription	Adipose Nuclei	Adipose
17	chr6:35350200-35359400	Weak transcription	Liver	Liver
18	chr6:35350400-35358400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:35351000-35357800	Weak transcription	Right Atrium	heart
20	chr6:35351000-35359000	Weak transcription	Primary T cells from cord blood	blood
21	chr6:35351000-35359200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:35351000-35359400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:35351000-35360200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:35351000-35360800	Weak transcription	Primary B cells from cord blood	blood
25	chr6:35351000-35363400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:35351200-35356400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:35351200-35357600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:35351200-35357800	Weak transcription	Dnd41	blood
29	chr6:35351200-35359200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:35351200-35359400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:35351200-35359600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:35353600-35358000	Enhancers	Placenta	Placenta
33	chr6:35353800-35359000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:35354000-35356400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:35354000-35356400	Weak transcription	Colonic Mucosa	Colon
36	chr6:35354000-35356400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:35354000-35356400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:35354000-35356600	Weak transcription	Small Intestine	intestine
39	chr6:35354000-35357600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:35354000-35357600	Weak transcription	HMEC	breast
41	chr6:35354000-35357800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:35354000-35358400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr6:35354000-35358400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:35354000-35358600	Weak transcription	NHLF	lung
45	chr6:35354000-35359000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:35354000-35359200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:35354000-35359200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr6:35354000-35359200	Weak transcription	Fetal Lung	lung
49	chr6:35354000-35359200	Weak transcription	HSMMtube	muscle
50	chr6:35354000-35359400	Weak transcription	Left Ventricle	heart

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