Variant report

Variant	rs6678064
Chromosome Location	chr1:173383213-173383214
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173381848..173384240-chr1:173792983..173794563,2	K562	blood:
2	chr1:173383188..173385613-chr1:173387916..173390631,2	K562	blood:
3	chr1:173378386..173381395-chr1:173383017..173386939,3	K562	blood:
4	chr1:173381379..173384289-chr1:173385199..173387543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117593	Chromatin interaction
ENSG00000120334	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11799616	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809193	0.89[ASN][1000 genomes]
rs11811598	0.87[ASN][1000 genomes]
rs12085083	0.93[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap]
rs12562415	0.86[ASN][1000 genomes]
rs3934577	0.93[CHB][hapmap];0.82[CHD][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs55741047	0.83[ASN][1000 genomes]
rs57231379	0.87[ASN][1000 genomes]
rs57262055	0.83[ASN][1000 genomes]
rs60302114	0.81[ASN][1000 genomes]
rs6700269	0.93[CHB][hapmap]
rs6700499	0.86[ASN][1000 genomes]
rs6702339	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs72726915	0.83[ASN][1000 genomes]
rs74126390	0.83[ASN][1000 genomes]
rs7534736	0.86[CHB][hapmap];0.90[TSI][hapmap]
rs7538559	0.89[ASN][1000 genomes]
rs7555324	0.83[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	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6678064		cis	Lymphoblastoid	GTEx
rs6678064	CENPL	cis	lymphoblastoid	seeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173348600-173389400	Weak transcription	Right Ventricle	heart
2	chr1:173363800-173389400	Weak transcription	Fetal Lung	lung
3	chr1:173365000-173385200	Weak transcription	Fetal Stomach	stomach
4	chr1:173370800-173389200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:173370800-173389200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:173370800-173389400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:173370800-173389400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:173370800-173389400	Weak transcription	Aorta	Aorta
9	chr1:173372000-173398600	Weak transcription	Brain Substantia Nigra	brain
10	chr1:173375200-173398600	Weak transcription	Esophagus	oesophagus
11	chr1:173376000-173389400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:173376200-173389400	Weak transcription	Brain Anterior Caudate	brain
13	chr1:173376200-173429000	Weak transcription	Gastric	stomach
14	chr1:173376400-173384000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:173376400-173384600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:173376400-173385000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:173376400-173385200	Weak transcription	Lung	lung
18	chr1:173376400-173389000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:173376400-173389200	Weak transcription	Liver	Liver
20	chr1:173376400-173389200	Weak transcription	A549	lung
21	chr1:173376400-173389400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:173376400-173389400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:173376400-173389400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:173376400-173400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:173376600-173389200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:173376600-173389400	Weak transcription	Colonic Mucosa	Colon
27	chr1:173376600-173389600	Enhancers	Primary B cells from peripheral blood	blood
28	chr1:173376600-173392600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:173377800-173383600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:173378000-173384000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:173378200-173384600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:173378400-173398400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:173379000-173398400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:173379200-173393200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:173379600-173389200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:173380000-173389400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:173380000-173389600	Enhancers	Primary B cells from cord blood	blood
38	chr1:173380200-173383400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:173380200-173384800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:173380200-173386200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:173380200-173387200	Weak transcription	HepG2	liver
42	chr1:173380200-173389400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:173380200-173391200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:173380200-173398400	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:173380200-173398600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:173380200-173398600	Weak transcription	Psoas Muscle	Psoas
47	chr1:173380400-173383800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:173380400-173386200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:173380400-173386800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:173380400-173387400	Weak transcription	HSMM	muscle

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