Variant report

Variant	rs4717329
Chromosome Location	chr7:66354384-66354385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr7:66354143-66354487	T-47D	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCTD7-2	chr7:66352258-66355627	NONHSAT121240

Variant related genes	Relation type
RNU6-1254P	TF binding region

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs12531402	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12531516	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12531690	0.82[EUR][1000 genomes]
rs12532147	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12532160	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes]
rs12532650	0.81[AMR][1000 genomes]
rs12533830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12533886	0.80[EUR][1000 genomes]
rs12534391	0.84[EUR][1000 genomes]
rs12534401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12534435	0.84[EUR][1000 genomes]
rs12535268	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12537403	0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs12537545	0.84[EUR][1000 genomes]
rs12537771	0.84[EUR][1000 genomes]
rs12537825	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12537955	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12538126	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12539191	0.84[EUR][1000 genomes]
rs12539366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12539522	0.84[EUR][1000 genomes]
rs12539848	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12540312	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12540447	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12540536	0.84[EUR][1000 genomes]
rs12540695	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes]
rs17138017	1.00[CEU][hapmap]
rs17230057	0.84[EUR][1000 genomes]
rs17567255	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2091314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286682	0.84[EUR][1000 genomes]
rs2286685	0.82[EUR][1000 genomes]
rs2286686	0.84[EUR][1000 genomes]
rs2293351	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34758320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778906	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3778911	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3800813	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs3800819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3823608	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4717309	0.84[EUR][1000 genomes]
rs4717311	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs4717312	0.84[EUR][1000 genomes]
rs4717313	0.84[EUR][1000 genomes]
rs4717314	0.84[EUR][1000 genomes]
rs4717316	0.84[EUR][1000 genomes]
rs4717323	0.81[AMR][1000 genomes]
rs4717324	0.87[AMR][1000 genomes]
rs4717332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4718390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs4718391	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs4718392	0.84[EUR][1000 genomes]
rs4718398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4718426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465688	0.87[AMR][1000 genomes]
rs62465698	0.87[AMR][1000 genomes]
rs62465699	0.87[AMR][1000 genomes]
rs62465700	0.81[AMR][1000 genomes]
rs62465701	0.81[AMR][1000 genomes]
rs62465705	0.81[AMR][1000 genomes]
rs62465706	0.87[AMR][1000 genomes]
rs62465707	0.87[AMR][1000 genomes]
rs62465709	0.87[AMR][1000 genomes]
rs62465710	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62465712	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62465713	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62465714	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62465716	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62465730	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62465734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62465736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62465752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62466091	0.84[EUR][1000 genomes]
rs62466122	0.84[EUR][1000 genomes]
rs62466123	0.84[EUR][1000 genomes]
rs62466126	0.84[EUR][1000 genomes]
rs62466127	0.84[EUR][1000 genomes]
rs62466128	0.84[EUR][1000 genomes]
rs62466133	0.84[EUR][1000 genomes]
rs62466134	0.84[EUR][1000 genomes]
rs62466136	0.84[EUR][1000 genomes]
rs62466137	0.84[EUR][1000 genomes]
rs62466138	0.84[EUR][1000 genomes]
rs62466139	0.84[EUR][1000 genomes]
rs62466142	0.82[EUR][1000 genomes]
rs62466143	0.82[EUR][1000 genomes]
rs62466144	0.84[EUR][1000 genomes]
rs62466145	0.84[EUR][1000 genomes]
rs62466146	0.84[EUR][1000 genomes]
rs62466147	0.84[EUR][1000 genomes]
rs62466148	0.84[EUR][1000 genomes]
rs62466575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62466578	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62466582	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466584	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466586	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62466588	0.87[AMR][1000 genomes]
rs62466589	0.87[AMR][1000 genomes]
rs62466787	0.84[EUR][1000 genomes]
rs62466788	0.84[EUR][1000 genomes]
rs62466789	0.84[EUR][1000 genomes]
rs62466792	0.84[EUR][1000 genomes]
rs62466795	0.84[EUR][1000 genomes]
rs62466797	0.84[EUR][1000 genomes]
rs62466798	0.84[EUR][1000 genomes]
rs62466799	0.80[EUR][1000 genomes]
rs62466801	0.84[EUR][1000 genomes]
rs62466802	0.84[EUR][1000 genomes]

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	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv981514	chr7:66310139-66366240	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4717329	RABGEF1	cis	multi-tissue	Pritchard
rs4717329	hmm32897	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66311000-66358400	Weak transcription	Brain Anterior Caudate	brain
2	chr7:66311000-66368000	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
5	chr7:66317200-66364400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:66319400-66364800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:66321200-66367800	Weak transcription	Aorta	Aorta
8	chr7:66322400-66364200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:66324400-66363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:66325200-66360200	Weak transcription	Psoas Muscle	Psoas
11	chr7:66325200-66366400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:66325400-66366400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:66325400-66369400	Weak transcription	Fetal Brain Female	brain
14	chr7:66325600-66359000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:66325600-66363600	Weak transcription	Primary B cells from cord blood	blood
16	chr7:66325600-66363600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:66325600-66373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:66325800-66359600	Weak transcription	Spleen	Spleen
19	chr7:66325800-66363400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr7:66325800-66363400	Weak transcription	Brain Substantia Nigra	brain
21	chr7:66325800-66365800	Weak transcription	Esophagus	oesophagus
22	chr7:66325800-66366400	Weak transcription	Right Ventricle	heart
23	chr7:66325800-66367000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:66325800-66367600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:66326000-66362000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:66326000-66363600	Weak transcription	Gastric	stomach
27	chr7:66326400-66358200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:66326400-66362600	Weak transcription	Brain Hippocampus Middle	brain
29	chr7:66326400-66363000	Weak transcription	Lung	lung
30	chr7:66326400-66368200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:66326400-66371800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:66326600-66363000	Weak transcription	Fetal Stomach	stomach
33	chr7:66328200-66367000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:66329600-66362000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:66329800-66372000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr7:66330400-66366000	Weak transcription	Fetal Thymus	thymus
37	chr7:66331800-66378400	Weak transcription	A549	lung
38	chr7:66333000-66371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:66333800-66364000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:66333800-66371800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr7:66334200-66367600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr7:66335000-66361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:66335000-66363800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr7:66335400-66371400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr7:66335600-66361400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:66335600-66363800	Weak transcription	Adipose Nuclei	Adipose
47	chr7:66336200-66364600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:66336200-66366400	Weak transcription	Thymus	Thymus
49	chr7:66336200-66369400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:66340800-66361200	Weak transcription	Fetal Lung	lung

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