Variant report

Variant	rs4707380
Chromosome Location	chr6:88311975-88311976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88310992..88313327-chr6:88328305..88330918,2	K562	blood:
2	chr6:88301522..88303882-chr6:88310493..88312545,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11965607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12663400	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13213729	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13220363	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35773999	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4330517	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4552702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748693	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7756133	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7768566	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7772351	0.94[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs910267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444515	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444529	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450725	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450727	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450730	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450731	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450756	0.82[CHB][hapmap]
rs9450757	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450759	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450765	0.87[AMR][1000 genomes];0.93[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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4707380	KDM5D	trans	lymphoblastoid	seeQTL
rs4707380	C6orf162	cis	parietal	SCAN
rs4707380	SLC35A1	cis	multi-tissue	Pritchard
rs4707380	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs4707380	RPS4Y1	trans	lymphoblastoid	seeQTL
rs4707380	DDX3Y	trans	lymphoblastoid	seeQTL
rs4707380	SLC35A1	cis	parietal	SCAN
rs4707380	SLC35A1	cis	lymphoblastoid	seeQTL
rs4707380	HDHD1	trans	lymphoblastoid	seeQTL
rs4707380	UTY	trans	lymphoblastoid	seeQTL
rs4707380	EIF1AY	trans	lymphoblastoid	seeQTL
rs4707380	CYorf15B	trans	lymphoblastoid	seeQTL
rs4707380	AKIRIN2	cis	cerebellum	SCAN
rs4707380	C6orf162	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300400-88320800	Weak transcription	Spleen	Spleen
2	chr6:88300400-88323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:88300600-88315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:88300600-88320000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:88300600-88321800	Weak transcription	Lung	lung
6	chr6:88300600-88323400	Weak transcription	Gastric	stomach
7	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
8	chr6:88300800-88320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:88300800-88323600	Weak transcription	Aorta	Aorta
10	chr6:88301000-88313800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:88301000-88315600	Weak transcription	NH-A	brain
12	chr6:88301000-88316400	Weak transcription	Pancreas	Pancrea
13	chr6:88301000-88321000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:88301000-88321000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:88301000-88323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:88301000-88330200	Weak transcription	Right Ventricle	heart
17	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
18	chr6:88301200-88313000	Weak transcription	NHDF-Ad	bronchial
19	chr6:88301200-88313200	Weak transcription	Hela-S3	cervix
20	chr6:88301200-88314000	Weak transcription	HMEC	breast
21	chr6:88301200-88316200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:88301200-88320800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:88301200-88320800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:88301200-88323400	Weak transcription	Thymus	Thymus
25	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:88301400-88313000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:88301400-88320800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:88301400-88321000	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:88301400-88322400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:88301400-88338400	Weak transcription	NHLF	lung
31	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:88301600-88320800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:88301800-88319800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:88302800-88318800	Weak transcription	HepG2	liver
39	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:88305200-88316200	Weak transcription	K562	blood
41	chr6:88305200-88329000	Weak transcription	HSMMtube	muscle
42	chr6:88305400-88313800	Weak transcription	A549	lung
43	chr6:88305400-88315800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:88305400-88315800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:88305400-88316000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr6:88305400-88316000	Weak transcription	GM12878-XiMat	blood
47	chr6:88305400-88316200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr6:88305400-88317000	Weak transcription	Osteobl	bone
49	chr6:88305400-88317800	Weak transcription	Primary B cells from cord blood	blood
50	chr6:88305400-88320800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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