Variant report

Variant	rs916403
Chromosome Location	chr6:28408258-28408259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28407404..28409073-chr6:28410400..28412244,2	K562	blood:
2	chr6:28365707..28367245-chr6:28405846..28408516,2	K562	blood:
3	chr6:28382729..28384623-chr6:28406130..28408766,2	K562	blood:

Variant related genes	Relation type
ENSG00000187987	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1005125	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1052215	0.83[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap]
rs1124132	0.80[AMR][1000 genomes]
rs1361387	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2023493	0.82[AMR][1000 genomes]
rs213232	0.81[ASN][1000 genomes]
rs213236	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs213237	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[YRI][hapmap]
rs213240	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2247002	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2531803	0.94[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2531804	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2531805	0.86[AMR][1000 genomes]
rs2531806	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2531825	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2531831	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2531832	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2859365	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6899512	0.81[YRI][hapmap]
rs6912921	0.81[YRI][hapmap]
rs728122	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9301	0.83[CHB][hapmap]
rs9468372	0.84[ASN][1000 genomes]

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs916403	ZSCAN23	cis	lung	GTEx
rs916403	ZNF323	cis	parietal	SCAN
rs916403	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs916403	ZSCAN23	cis	Muscle Skeletal	GTEx
rs916403	ZSCAN23	cis	lymphoblastoid	seeQTL
rs916403	FAM65B	cis	cerebellum	SCAN
rs916403	ZKSCAN3	cis	parietal	SCAN
rs916403	AL022393.7	cis	Heart Left Ventricle	GTEx
rs916403	ZNF323	cis	cerebellum	SCAN
rs916403	AL022393.7	cis	Muscle Skeletal	GTEx
rs916403	ZNF192	cis	cerebellum	SCAN
rs916403	HIST1H2BN	cis	cerebellum	SCAN
rs916403	ZNF391	cis	cerebellum	SCAN
rs916403	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs916403	ZSCAN23	cis	cerebellum	SCAN
rs916403	ZSCAN23	Cis_1M	lymphoblastoid	RTeQTL
rs916403	AL022393.7	cis	lung	GTEx
rs916403	ZSCAN23	cis	parietal	SCAN
rs916403	ZSCAN23	cis	Nerve Tibial	GTEx
rs916403	ZSCAN23	cis	Esophagus Mucosa	GTEx
rs916403	AL022393.7	cis	Nerve Tibial	GTEx
rs916403	ZSCAN31	cis	lung	GTEx
rs916403	ZNF187	cis	cerebellum	SCAN
rs916403	ZSCAN23	cis	Stomach	GTEx
rs916403	ZSCAN23	cis	Artery Tibial	GTEx
rs916403	SLC17A1	cis	parietal	SCAN

Chromatin state (count:79 , 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	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:28385600-28410800	Weak transcription	Lung	lung
4	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
6	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
7	chr6:28389200-28410200	Weak transcription	NHLF	lung
8	chr6:28389400-28410000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:28389600-28409800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:28389600-28410200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:28389600-28410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:28389600-28410400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:28389800-28410800	Weak transcription	Colonic Mucosa	Colon
14	chr6:28390200-28410400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:28391400-28410400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:28391400-28410800	Weak transcription	Placenta	Placenta
17	chr6:28391600-28410200	Weak transcription	Brain Anterior Caudate	brain
18	chr6:28391600-28410800	Weak transcription	Pancreas	Pancrea
19	chr6:28392000-28410200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:28392000-28410400	Weak transcription	NHEK	skin
21	chr6:28392200-28410400	Weak transcription	Right Ventricle	heart
22	chr6:28392400-28410000	Weak transcription	HMEC	breast
23	chr6:28392400-28410400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:28393600-28410800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:28393800-28410600	Weak transcription	Aorta	Aorta
26	chr6:28394200-28409800	Weak transcription	Fetal Heart	heart
27	chr6:28395200-28410200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:28395400-28409400	Weak transcription	Fetal Brain Male	brain
29	chr6:28398000-28410800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:28398600-28410400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:28398600-28410600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:28399400-28410400	Weak transcription	HSMM	muscle
33	chr6:28400600-28410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:28402600-28410200	Weak transcription	Primary T cells from cord blood	blood
35	chr6:28402600-28410200	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:28402600-28410600	Weak transcription	HSMMtube	muscle
37	chr6:28402800-28410200	Weak transcription	Fetal Kidney	kidney
38	chr6:28402800-28410400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:28402800-28410600	Weak transcription	Ovary	ovary
40	chr6:28403200-28410200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:28403200-28410200	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:28403200-28410200	Weak transcription	Osteobl	bone
43	chr6:28403200-28410400	Weak transcription	NH-A	brain
44	chr6:28403400-28410000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:28403400-28410000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:28403400-28410200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:28403600-28409200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:28403600-28410200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:28403800-28410000	Weak transcription	Dnd41	blood
50	chr6:28403800-28410200	Weak transcription	H1 Cell Line	embryonic stem cell

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