Variant report

Variant	rs759272
Chromosome Location	chr7:27648241-27648242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27646394..27648572-chr7:27650317..27653232,2	K562	blood:
2	chr7:27646490..27649640-chr7:27701348..27703322,3	K562	blood:
3	chr7:27647308..27649264-chr7:27813060..27815813,2	K562	blood:
4	chr7:27646423..27648425-chr7:27891373..27893179,2	K562	blood:

Variant related genes	Relation type
ENSG00000106049	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1005418	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10486549	0.91[JPT][hapmap]
rs12667470	0.91[JPT][hapmap]
rs12670250	0.86[JPT][hapmap]
rs12671723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12674175	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12700831	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1524527	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1524531	0.84[YRI][hapmap]
rs16874305	0.95[CHB][hapmap]
rs17155443	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs17155498	0.86[JPT][hapmap]
rs17155505	0.86[JPT][hapmap]
rs17155537	0.91[JPT][hapmap]
rs17155705	0.81[CEU][hapmap]
rs17155836	0.80[CEU][hapmap]
rs2391437	0.84[EUR][1000 genomes]
rs2391450	0.86[JPT][hapmap]
rs2893292	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34536886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3735570	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3779472	0.80[CEU][hapmap]
rs42089	0.95[JPT][hapmap]
rs58231871	0.80[ASN][1000 genomes]
rs62456951	0.80[ASN][1000 genomes]
rs6462022	0.85[EUR][1000 genomes]
rs6462023	0.85[EUR][1000 genomes]
rs6950698	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6975900	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs759268	0.86[JPT][hapmap]
rs7778454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7779488	0.86[EUR][1000 genomes]
rs999491	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS 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 miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs759272	NEUROD6	cis	parietal	SCAN
rs759272	HIBADH	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
2	chr7:27609400-27651000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:27615600-27657800	Weak transcription	Aorta	Aorta
4	chr7:27616000-27650800	Weak transcription	Fetal Kidney	kidney
5	chr7:27626600-27654800	Weak transcription	Placenta	Placenta
6	chr7:27626800-27655800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:27628200-27658400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:27628600-27658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:27629600-27655400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:27630200-27654600	Weak transcription	Primary B cells from cord blood	blood
11	chr7:27630400-27656800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr7:27632200-27655600	Weak transcription	Primary T cells from cord blood	blood
13	chr7:27644200-27655400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:27644400-27649200	Enhancers	Fetal Intestine Small	intestine
15	chr7:27644400-27658400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr7:27645000-27649000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr7:27645400-27655600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:27646000-27655200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:27646200-27648400	Weak transcription	NHEK	skin
20	chr7:27646200-27649200	Enhancers	Fetal Intestine Large	intestine
21	chr7:27646200-27651800	Enhancers	Hela-S3	cervix
22	chr7:27646200-27655600	Weak transcription	Fetal Muscle Leg	muscle
23	chr7:27646200-27657800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr7:27646400-27648400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:27646400-27648600	Enhancers	HepG2	liver
26	chr7:27646400-27650800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:27646400-27650800	Weak transcription	NHDF-Ad	bronchial
28	chr7:27646400-27654800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:27646400-27655600	Weak transcription	Fetal Stomach	stomach
30	chr7:27646600-27648400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:27646600-27648400	Weak transcription	NH-A	brain
32	chr7:27646600-27648800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr7:27646600-27649200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:27646600-27649200	Enhancers	HUVEC	blood vessel
35	chr7:27646600-27656600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:27646600-27658400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:27646800-27648400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:27646800-27649400	Enhancers	A549	lung
39	chr7:27646800-27650200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:27646800-27650400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:27646800-27655600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:27646800-27657800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:27646800-27658800	Weak transcription	Osteobl	bone
44	chr7:27646800-27659600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr7:27647000-27648400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:27647000-27648800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr7:27647000-27650400	Weak transcription	Fetal Lung	lung
48	chr7:27647000-27655800	Weak transcription	Ovary	ovary
49	chr7:27647000-27657200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:27647000-27660200	Weak transcription	Small Intestine	intestine

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