Variant report

Variant	rs157778
Chromosome Location	chr15:76759444-76759445
allele	C/G
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	chr15:76759385-76759969	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000261232	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs157757	0.87[CEU][hapmap]
rs157760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157762	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157763	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs157766	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs157768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs157769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs157775	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157779	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs157788	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs157789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs166906	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs166933	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16968196	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs172244	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1810348	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs182253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875883	0.83[EUR][1000 genomes]
rs190771	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2078437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439984	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs2439992	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs2456066	0.87[CEU][hapmap]
rs2460158	0.85[CEU][hapmap]
rs2460161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2468122	0.87[CEU][hapmap]
rs2468123	0.92[YRI][hapmap]
rs2468129	0.82[AFR][1000 genomes]
rs2469211	0.87[CEU][hapmap]
rs2469214	0.87[CEU][hapmap]
rs2469215	0.85[CEU][hapmap]
rs2469224	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2469535	0.81[ASN][1000 genomes]
rs2469539	0.87[CEU][hapmap]
rs2469554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2469556	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2469573	0.87[CEU][hapmap]
rs283796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs283802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284884	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284893	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284901	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938695	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2944377	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2948703	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2956873	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2956875	0.87[CEU][hapmap]
rs2957560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957611	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2957612	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957613	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs387321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs403656	1.00[JPT][hapmap]
rs438915	0.82[ASN][1000 genomes]
rs454381	0.90[ASN][1000 genomes]
rs480672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4886490	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs4886491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs494268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs506000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8031378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8031672	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8042255	0.87[CEU][hapmap]
rs874224	0.87[CEU][hapmap];0.90[CHB][hapmap]

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	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs157778	ISL2	cis	Whole Blood	GTEx
rs157778	RP11-685G9.2	cis	Whole Blood	GTEx
rs157778	ISL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76711600-76767200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:76720800-76763600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
4	chr15:76742800-76762400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:76750400-76763800	Weak transcription	Placenta	Placenta
6	chr15:76753200-76762800	Weak transcription	Esophagus	oesophagus
7	chr15:76753400-76760800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:76753600-76761600	Weak transcription	Adipose Nuclei	Adipose
9	chr15:76753800-76764400	Weak transcription	Fetal Intestine Large	intestine
10	chr15:76754000-76764400	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:76754200-76763600	Weak transcription	Pancreas	Pancrea
12	chr15:76754400-76763600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:76754800-76762000	Weak transcription	Ovary	ovary
14	chr15:76754800-76764400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:76755200-76761200	Weak transcription	Brain Anterior Caudate	brain
16	chr15:76755600-76764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:76757400-76760200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:76757600-76759600	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr15:76757800-76765200	Weak transcription	Aorta	Aorta
20	chr15:76758400-76765600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:76758600-76761200	Weak transcription	Fetal Heart	heart
22	chr15:76758600-76762400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:76758800-76764400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:76758800-76765000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:76758800-76765200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:76759000-76760000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr15:76759000-76761000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr15:76759200-76760000	ZNF genes & repeats	GM12878-XiMat	blood
29	chr15:76759200-76762600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:76759200-76763800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:76759200-76764400	Weak transcription	Psoas Muscle	Psoas
32	chr15:76759400-76760800	Weak transcription	Primary B cells from cord blood	blood
33	chr15:76759400-76761800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:76759400-76762600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:76759400-76763600	Strong transcription	Liver	Liver
36	chr15:76759400-76764400	Weak transcription	Fetal Muscle Leg	muscle

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