Variant report

Variant	rs6691053
Chromosome Location	chr1:173868955-173868956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173859716..173863027-chr1:173865455..173870785,5	K562	blood:
2	chr1:173865468..173869830-chr1:173871500..173875883,4	MCF-7	breast:
3	chr1:173868345..173870292-chr1:173879579..173881405,2	K562	blood:
4	chr1:173868704..173870321-chr1:173875152..173876806,2	K562	blood:
5	chr1:173813848..173815354-chr1:173868655..173871235,2	MCF-7	breast:
6	chr1:173865064..173869391-chr1:173883979..173888192,4	MCF-7	breast:
7	chr1:173805772..173808648-chr1:173867420..173869659,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117601	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16846526	0.82[CHB][hapmap]
rs16846546	0.82[CHB][hapmap];0.80[LWK][hapmap]
rs16846561	0.82[CHB][hapmap];0.80[LWK][hapmap]
rs1951626	0.94[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2065170	0.82[CHB][hapmap]
rs2227589	0.82[CHB][hapmap]
rs2227592	0.82[CHB][hapmap]
rs2759328	0.82[CHB][hapmap]
rs28680958	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6698314	0.81[MEX][hapmap]
rs7525115	0.81[MEX][hapmap]
rs941988	0.82[CHB][hapmap]

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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6691053	dJ383J4.3	cis	multi-tissue	Pritchard
rs6691053	SELP	cis	cerebellum	SCAN
rs6691053	C1orf105	cis	cerebellum	SCAN
rs6691053	CENPL	cis	lymphoblastoid	seeQTL
rs6691053	SNORD78	cis	parietal	SCAN
rs6691053		cis	Lymphoblastoid	GTEx
rs6691053	TNFSF18	cis	cerebellum	SCAN
rs6691053	MRPS14	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173855600-173875400	Weak transcription	NH-A	brain
2	chr1:173855800-173873000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:173855800-173880400	Weak transcription	Thymus	Thymus
4	chr1:173856000-173869400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:173856000-173869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:173856000-173872600	Weak transcription	Fetal Thymus	thymus
7	chr1:173856000-173883000	Weak transcription	Right Ventricle	heart
8	chr1:173856200-173869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:173856200-173872800	Weak transcription	Ovary	ovary
10	chr1:173856200-173875400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:173856200-173878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:173856200-173880400	Weak transcription	Psoas Muscle	Psoas
13	chr1:173856400-173873800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:173856400-173876000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:173856400-173880000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:173856600-173881200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
18	chr1:173857000-173883800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:173857400-173869000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:173857400-173869400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:173857400-173880400	Weak transcription	Fetal Brain Female	brain
22	chr1:173857400-173881800	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:173857400-173884400	Weak transcription	HepG2	liver
24	chr1:173857400-173885800	Weak transcription	Fetal Intestine Large	intestine
25	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
26	chr1:173857600-173870000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:173857600-173872600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
29	chr1:173858400-173878600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:173858600-173881400	Weak transcription	Primary B cells from cord blood	blood
31	chr1:173858600-173886800	Weak transcription	Placenta	Placenta
32	chr1:173858800-173871400	Weak transcription	HSMM	muscle
33	chr1:173858800-173872200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:173858800-173876000	Weak transcription	NHLF	lung
35	chr1:173860200-173869000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:173860200-173869200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:173862000-173873400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:173862000-173891600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:173862200-173872000	Weak transcription	Fetal Lung	lung
40	chr1:173863600-173875800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:173863800-173878800	Weak transcription	Aorta	Aorta
42	chr1:173864000-173875600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:173864200-173878600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:173864600-173869600	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:173864600-173871800	Weak transcription	Fetal Stomach	stomach
46	chr1:173864600-173878200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:173864600-173886600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:173865200-173874600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:173865400-173869400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:173865400-173873200	Weak transcription	Primary T cells from cord blood	blood

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