Variant report

Variant	rs2531831
Chromosome Location	chr6:28388765-28388766
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28356707..28359445-chr6:28388134..28391982,4	K562	blood:
2	chr6:28356866..28359445-chr6:28388346..28391982,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005125	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052215	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10946954	0.90[EUR][1000 genomes]
rs1124132	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1150705	0.81[EUR][1000 genomes]
rs1150707	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1150709	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1150716	0.84[EUR][1000 genomes]
rs12214383	0.81[CEU][hapmap]
rs1233713	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13408	0.81[CEU][hapmap]
rs1361387	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1531681	0.81[CEU][hapmap]
rs1558205	0.83[TSI][hapmap]
rs1736895	0.81[CEU][hapmap]
rs2023493	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2108927	0.80[EUR][1000 genomes]
rs213232	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs213236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs213237	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs213238	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs213240	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs2142730	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2247002	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531803	0.87[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2531804	0.80[GIH][hapmap]
rs2531805	0.80[AMR][1000 genomes]
rs2531806	0.84[AMR][1000 genomes]
rs2531825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2531832	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2859348	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs2859365	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4455662	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6899512	0.81[YRI][hapmap]
rs6912921	0.81[YRI][hapmap]
rs7206	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs728122	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853684	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs916403	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9301	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs9368565	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468372	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[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	esv1836974	chr6:28376981-28398748	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs2531831	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs2531831	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs2531831	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs2531831	ZSCAN23	cis	lung	GTEx
rs2531831	ZNF96	cis	multi-tissue	Pritchard
rs2531831	AL022393.7	cis	Esophagus Muscularis	GTEx
rs2531831	ZSCAN23	cis	Muscle Skeletal	GTEx
rs2531831	AL022393.7	cis	Muscle Skeletal	GTEx
rs2531831	AL022393.7	cis	Heart Left Ventricle	GTEx
rs2531831	ZSCAN23	cis	lymphoblastoid	seeQTL
rs2531831	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs2531831	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs2531831	ZSCAN31	cis	Muscle Skeletal	GTEx
rs2531831	ZSCAN23	cis	Artery Tibial	GTEx
rs2531831	ZSCAN31	cis	Thyroid	GTEx
rs2531831	ZSCAN31	cis	lung	GTEx
rs2531831	ZNF323	cis	Frontal Cortex	GTEx
rs2531831	AL022393.7	cis	lung	GTEx
rs2531831	AL022393.7	cis	Nerve Tibial	GTEx
rs2531831	RP5-874C20.3	cis	Thyroid	GTEx
rs2531831	ZSCAN23	cis	Stomach	GTEx
rs2531831	AL022393.7	cis	Artery Tibial	GTEx
rs2531831	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs2531831	AL022393.7	cis	Artery Aorta	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28377600-28390200	Weak transcription	Fetal Lung	lung
3	chr6:28379400-28389200	Weak transcription	HSMM	muscle
4	chr6:28380800-28390600	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:28381400-28390000	Weak transcription	Fetal Brain Female	brain
6	chr6:28383400-28390600	Weak transcription	Fetal Stomach	stomach
7	chr6:28383600-28392600	Weak transcription	Brain Germinal Matrix	brain
8	chr6:28383800-28393000	Weak transcription	Fetal Intestine Small	intestine
9	chr6:28384600-28390200	Weak transcription	NH-A	brain
10	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:28384800-28390800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:28385000-28390600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:28385200-28390600	Weak transcription	Placenta	Placenta
14	chr6:28385400-28391000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:28385400-28391200	Weak transcription	HSMMtube	muscle
16	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
17	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:28385600-28390800	Weak transcription	Aorta	Aorta
19	chr6:28385600-28390800	Weak transcription	Ovary	ovary
20	chr6:28385600-28410800	Weak transcription	Lung	lung
21	chr6:28385800-28390800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:28385800-28391800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:28386000-28402200	Weak transcription	Osteobl	bone
24	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:28386200-28390000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:28386200-28390600	Weak transcription	Right Ventricle	heart
27	chr6:28386200-28391000	Weak transcription	Psoas Muscle	Psoas
28	chr6:28386200-28395800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:28386600-28391000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:28386600-28392200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:28386600-28392800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:28386600-28397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:28386800-28392000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:28386800-28393600	Weak transcription	Fetal Heart	heart
35	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:28387400-28390600	Weak transcription	Fetal Intestine Large	intestine
37	chr6:28387600-28393000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:28387600-28394200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:28387800-28390600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:28387800-28390600	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:28387800-28390800	Weak transcription	Brain Anterior Caudate	brain
42	chr6:28387800-28393000	Weak transcription	Fetal Brain Male	brain
43	chr6:28387800-28395400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
45	chr6:28388000-28389800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:28388000-28390000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:28388000-28392800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
49	chr6:28388400-28390600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:28388400-28393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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