Variant report

Variant	rs2957560
Chromosome Location	chr15:76700310-76700311
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs157757	0.85[YRI][hapmap]
rs157760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs157761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs157762	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs157763	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs157766	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs157768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs157769	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs157775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs157777	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs157779	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs157788	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs157789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs166906	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs166933	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16968196	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172244	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1810348	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs182253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1875883	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs190771	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2078437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469224	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469535	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2469556	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs283796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs283799	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283802	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs284884	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs284885	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284886	0.81[ASN][1000 genomes]
rs284893	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284897	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284901	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs284907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2938695	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2944377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2948703	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2956873	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957611	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957613	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs403656	1.00[JPT][hapmap]
rs454381	0.90[ASN][1000 genomes]
rs480672	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886490	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs4886491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494268	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs506000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8031378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8031672	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874224	0.88[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510667	chr15:76653359-76708310	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
rs2957560	RP11-685G9.2	cis	Whole Blood	GTEx
rs2957560	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2957560	ISL2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76639800-76727400	Weak transcription	Right Ventricle	heart
2	chr15:76661000-76708600	Weak transcription	Brain Anterior Caudate	brain
3	chr15:76661200-76710800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:76666200-76706800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:76673200-76727400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:76674600-76718400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:76682600-76713800	Weak transcription	Fetal Intestine Small	intestine
8	chr15:76684800-76718200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:76691000-76703600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:76693600-76720400	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:76695600-76711000	Weak transcription	Lung	lung
12	chr15:76695800-76705800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:76695800-76706000	Weak transcription	Fetal Intestine Large	intestine
14	chr15:76695800-76709800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:76695800-76726000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:76696600-76720600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:76697000-76700400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:76697000-76700400	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:76697000-76703800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:76697000-76704800	Weak transcription	Fetal Thymus	thymus
21	chr15:76697000-76705000	Weak transcription	Primary B cells from cord blood	blood
22	chr15:76697000-76710400	Weak transcription	Left Ventricle	heart
23	chr15:76697000-76711000	Weak transcription	Esophagus	oesophagus
24	chr15:76697000-76718400	Weak transcription	Ovary	ovary
25	chr15:76697000-76719200	Weak transcription	Primary T cells from cord blood	blood
26	chr15:76697000-76720800	Weak transcription	Aorta	Aorta
27	chr15:76697000-76722200	Weak transcription	Spleen	Spleen
28	chr15:76697000-76723400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:76697000-76724000	Weak transcription	Brain Substantia Nigra	brain
30	chr15:76697000-76724400	Weak transcription	Pancreas	Pancrea
31	chr15:76697000-76726000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:76697000-76726400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:76697200-76706000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:76697200-76706800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:76697200-76720400	Weak transcription	Liver	Liver
36	chr15:76698400-76703200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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