Variant report

Variant	rs6692228
Chromosome Location	chr1:150904712-150904713
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150897904..150900695-chr1:150901454..150905304,5	K562	blood:
2	chr1:150903857..150905968-chr1:151042810..151044624,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143379	Chromatin interaction
ENSG00000143458	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2867296	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs6692228	CTSS	cis	multi-tissue	Pritchard
rs6692228	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs6692228	CTSS	cis	Thyroid	GTEx
rs6692228	RP11-316M1.12	cis	Whole Blood	GTEx
rs6692228	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6692228	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs6692228	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs6692228	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs6692228	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6692228	RP11-316M1.12	cis	Artery Tibial	GTEx
rs6692228	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs6692228	RP11-316M1.12	cis	Thyroid	GTEx
rs6692228	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs6692228	RP11-316M1.12	cis	Artery Aorta	GTEx
rs6692228	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6692228	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6692228	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs6692228	RP11-316M1.12	cis	lung	GTEx
rs6692228	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6692228	GOLPH3L	cis	Nerve Tibial	GTEx
rs6692228	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs6692228	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6692228	CTSS	cis	Artery Tibial	GTEx
rs6692228	HORMAD1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150899400-150915000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:150899600-150913200	Weak transcription	Aorta	Aorta
3	chr1:150899600-150913200	Weak transcription	Right Ventricle	heart
4	chr1:150899600-150913600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:150899600-150943400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:150900000-150905400	Strong transcription	NHDF-Ad	bronchial
7	chr1:150900000-150905600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:150900000-150905600	Strong transcription	Osteobl	bone
9	chr1:150900000-150905800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:150900000-150906200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:150900000-150913400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:150900000-150915200	Weak transcription	Esophagus	oesophagus
13	chr1:150900200-150905200	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr1:150900200-150905600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr1:150900200-150905800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:150900200-150905800	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr1:150900200-150906000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:150900200-150906000	Strong transcription	Fetal Kidney	kidney
19	chr1:150900200-150906000	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:150900200-150906200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:150900200-150906200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:150900200-150906600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:150900200-150908400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:150900200-150909000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:150900200-150941800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:150900400-150904800	Strong transcription	Left Ventricle	heart
27	chr1:150900400-150905400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:150900400-150906000	Strong transcription	Brain Hippocampus Middle	brain
29	chr1:150900400-150906000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:150900400-150906200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr1:150900400-150928400	Strong transcription	Liver	Liver
32	chr1:150900400-150941000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:150900400-150942600	Weak transcription	Stomach Mucosa	stomach
34	chr1:150900400-150944200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:150900600-150905800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:150900600-150906200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:150901000-150941600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:150901600-150941600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:150901800-150905400	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr1:150902000-150905400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:150902000-150905400	Strong transcription	Brain Substantia Nigra	brain
42	chr1:150902000-150905600	Strong transcription	NH-A	brain
43	chr1:150902000-150906000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:150902000-150906000	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr1:150902000-150906200	Strong transcription	HUVEC	blood vessel
46	chr1:150902200-150904800	Strong transcription	Colon Smooth Muscle	Colon
47	chr1:150902200-150905800	ZNF genes & repeats	GM12878-XiMat	blood
48	chr1:150902400-150904800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr1:150902400-150905200	Strong transcription	Rectal Smooth Muscle	rectum
50	chr1:150902400-150905400	ZNF genes & repeats	K562	blood

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