Variant report

Variant	rs2859348
Chromosome Location	chr6:28359170-28359171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28317708..28320040-chr6:28358361..28360220,2	K562	blood:
2	chr6:28046681..28048670-chr6:28358880..28361224,2	K562	blood:
3	chr6:28356707..28359445-chr6:28388134..28391982,4	K562	blood:
4	chr6:28356866..28359445-chr6:28388346..28391982,3	K562	blood:
5	chr6:28303466..28305009-chr6:28358955..28361935,2	K562	blood:
6	chr6:28352795..28355228-chr6:28357917..28359743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189298	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1005125	0.86[CEU][hapmap];0.90[AMR][1000 genomes]
rs1052215	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10946954	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1124132	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1150690	0.81[AFR][1000 genomes]
rs1150705	0.83[CHB][hapmap]
rs1150707	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs1150709	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs1150711	0.86[CHB][hapmap]
rs1150718	0.91[CHB][hapmap]
rs1150721	0.91[CHB][hapmap]
rs1150724	0.91[CHB][hapmap]
rs1150726	0.91[CHB][hapmap]
rs12214383	0.86[CHB][hapmap]
rs1233713	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs13408	0.86[CHB][hapmap]
rs1531681	0.86[CHB][hapmap]
rs1736891	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs1736895	0.86[CHB][hapmap]
rs1778484	0.86[CHB][hapmap]
rs1997660	0.91[CHB][hapmap]
rs2023493	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs213236	0.89[CEU][hapmap];0.80[CHB][hapmap]
rs213237	0.88[CEU][hapmap]
rs213238	0.82[CEU][hapmap];0.80[CHB][hapmap]
rs213240	0.84[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes]
rs2142730	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs2247002	0.83[AMR][1000 genomes]
rs2394049	0.91[CHB][hapmap]
rs2531805	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2531806	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2531825	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs2531831	0.83[AMR][1000 genomes]
rs2531832	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2859365	0.83[AMR][1000 genomes]
rs4455662	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs707907	0.91[CHB][hapmap]
rs7206	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs728122	0.81[AMR][1000 genomes]
rs853683	0.91[CHB][hapmap]
rs853684	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs853690	0.91[CHB][hapmap]
rs853693	0.91[CHB][hapmap]
rs9301	0.86[CHB][hapmap]
rs9368565	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9468333	0.91[CHB][hapmap]

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2859348	AL022393.7	cis	Esophagus Muscularis	GTEx
rs2859348	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs2859348	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs2859348	AL022393.7	cis	Artery Aorta	GTEx
rs2859348	AL022393.7	cis	Muscle Skeletal	GTEx
rs2859348	ZSCAN12	cis	brain	BrainEAC
rs2859348	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs2859348	ZSCAN31	cis	Stomach	GTEx
rs2859348	ZSCAN31	cis	lung	GTEx
rs2859348	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs2859348	ZSCAN23	cis	Artery Tibial	GTEx
rs2859348	RP5-874C20.3	cis	Thyroid	GTEx
rs2859348	ZSCAN31	cis	Thyroid	GTEx
rs2859348	AL022393.7	cis	Heart Left Ventricle	GTEx
rs2859348	ZSCAN23	cis	Muscle Skeletal	GTEx
rs2859348	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs2859348	AL022393.7	cis	Nerve Tibial	GTEx
rs2859348	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs2859348	ZSCAN23	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28345000-28361600	Strong transcription	Dnd41	blood
2	chr6:28351600-28364600	Weak transcription	Right Atrium	heart
3	chr6:28352000-28362000	Strong transcription	Primary T cells from cord blood	blood
4	chr6:28352200-28365800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:28352400-28361400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:28352600-28361800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:28352600-28362000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:28352600-28362600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:28352600-28364200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:28352600-28364400	Strong transcription	Fetal Thymus	thymus
11	chr6:28352600-28364600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:28352600-28365400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:28352600-28365800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:28352800-28361000	Strong transcription	Brain Anterior Caudate	brain
15	chr6:28353000-28359400	Strong transcription	Fetal Brain Female	brain
16	chr6:28353000-28361000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:28353000-28361000	Strong transcription	Fetal Intestine Large	intestine
18	chr6:28353000-28361400	Strong transcription	Brain Germinal Matrix	brain
19	chr6:28353000-28361600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:28353000-28361800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:28353000-28362200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:28353000-28364800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:28353200-28361200	Strong transcription	HepG2	liver
24	chr6:28353200-28361400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:28353200-28362000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:28353400-28361000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:28353400-28361200	Strong transcription	Liver	Liver
28	chr6:28353600-28359600	Strong transcription	Brain Cingulate Gyrus	brain
29	chr6:28353600-28360800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:28353800-28361200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:28354000-28364600	Strong transcription	Fetal Muscle Leg	muscle
32	chr6:28354200-28361800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr6:28354200-28365600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr6:28354400-28361000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:28354400-28364800	Strong transcription	Fetal Stomach	stomach
36	chr6:28354800-28360800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:28354800-28361400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:28354800-28363800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:28355000-28359400	Strong transcription	Lung	lung
40	chr6:28355000-28359400	Strong transcription	Thymus	Thymus
41	chr6:28355000-28359600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:28355000-28361000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:28355000-28361000	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr6:28355000-28361200	Strong transcription	HMEC	breast
45	chr6:28355000-28361400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr6:28355000-28361600	Strong transcription	Brain Hippocampus Middle	brain
47	chr6:28355200-28359600	Strong transcription	Left Ventricle	heart
48	chr6:28355200-28361400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:28355400-28360800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:28355400-28361800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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