Variant report

Variant	rs4729408
Chromosome Location	chr7:97772658-97772659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97770445..97772942-chr7:97776101..97777659,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1039057	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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11761896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11762771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11762810	0.88[EUR][1000 genomes]
rs11768678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11772060	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11773169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532380	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17169325	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2394824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729404	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55761857	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55765204	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56006208	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56034325	0.95[EUR][1000 genomes]
rs56088922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56174823	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56389625	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58911561	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62479768	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62479773	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62479795	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62479797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73149199	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs740208	0.87[EUR][1000 genomes]
rs884897	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4729408	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL
rs4729408	AKAP8	trans	lymphoblastoid	RTeQTL
rs4729408	FIS1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97745600-97781600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:97752600-97780800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:97761400-97781000	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:97762600-97793000	Weak transcription	Fetal Heart	heart
5	chr7:97763200-97792600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:97763400-97775000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:97763400-97801000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:97763400-97821000	Weak transcription	NHLF	lung
9	chr7:97763600-97788400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr7:97763600-97793000	Weak transcription	NH-A	brain
11	chr7:97763600-97814200	Weak transcription	Osteobl	bone
12	chr7:97763600-97815800	Weak transcription	HSMM	muscle
13	chr7:97763800-97784000	Weak transcription	HUVEC	blood vessel
14	chr7:97764000-97806200	Weak transcription	Psoas Muscle	Psoas
15	chr7:97764400-97780800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:97765400-97780800	Weak transcription	Brain Angular Gyrus	brain
17	chr7:97765800-97840800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr7:97766000-97773600	Strong transcription	Primary T cells from cord blood	blood
19	chr7:97766000-97776200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr7:97766000-97778400	Weak transcription	Small Intestine	intestine
21	chr7:97766000-97778800	Strong transcription	Dnd41	blood
22	chr7:97766000-97795000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:97766200-97773800	Strong transcription	Fetal Intestine Small	intestine
24	chr7:97766200-97774200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:97766200-97781600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:97766200-97790000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:97766400-97775000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:97766400-97786000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:97766600-97772800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:97766600-97773600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:97766600-97798400	Weak transcription	HSMMtube	muscle
32	chr7:97766800-97773400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:97766800-97774400	Strong transcription	Fetal Intestine Large	intestine
34	chr7:97766800-97774400	Strong transcription	Fetal Thymus	thymus
35	chr7:97766800-97775000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:97766800-97777000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:97767000-97773000	Strong transcription	Left Ventricle	heart
38	chr7:97767000-97773000	Strong transcription	HepG2	liver
39	chr7:97767000-97773200	Strong transcription	Fetal Muscle Leg	muscle
40	chr7:97767000-97774600	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr7:97767200-97773200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:97767200-97774600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:97767200-97775400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:97767400-97773200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:97767800-97781200	Weak transcription	A549	lung
46	chr7:97767800-97781400	Weak transcription	GM12878-XiMat	blood
47	chr7:97767800-97781400	Weak transcription	HMEC	breast
48	chr7:97768200-97780800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr7:97768200-97784200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr7:97768600-97774800	Weak transcription	Fetal Lung	lung

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