Variant report

Variant	rs2065170
Chromosome Location	chr1:173845232-173845233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173845188..173847906-chr1:173855416..173857290,2	MCF-7	breast:
2	chr1:173842881..173845710-chr1:173854372..173856048,2	K562	blood:
3	chr1:173844210..173845835-chr1:173854372..173856264,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16846418	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16846433	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846478	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846593	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2068871	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146372	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2235095	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2759328	1.00[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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791021	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791022	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs57022387	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58994962	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59393482	0.83[AMR][1000 genomes]
rs60689957	0.83[AMR][1000 genomes]
rs61262741	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61649485	0.84[ASN][1000 genomes]
rs6656255	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685043	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6691053	0.82[CHB][hapmap]
rs6696381	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941987	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[GIH][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs941988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970048	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2065170	CENPL	cis	lymphoblastoid	seeQTL
rs2065170	SNORD80	cis	parietal	SCAN
rs2065170	SNORD78	cis	parietal	SCAN
rs2065170	dJ383J4.3	cis	multi-tissue	Pritchard
rs2065170		cis	Lymphoblastoid	GTEx
rs2065170	SNORD79	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838200-173846600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:173838200-173854200	Weak transcription	Gastric	stomach
3	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
4	chr1:173838400-173854200	Weak transcription	Esophagus	oesophagus
5	chr1:173838400-173854800	Weak transcription	Aorta	Aorta
6	chr1:173838400-173854800	Weak transcription	Right Ventricle	heart
7	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:173838600-173854800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:173838800-173855800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:173839000-173848400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:173839000-173850000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:173839000-173854800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:173839000-173862800	Weak transcription	HMEC	breast
14	chr1:173839200-173850000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:173839200-173855000	Weak transcription	A549	lung
16	chr1:173839400-173847800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr1:173839400-173847800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:173839400-173849200	Strong transcription	Fetal Stomach	stomach
19	chr1:173839400-173850000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:173839600-173854600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:173839800-173845400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:173840000-173845400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:173840200-173845800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:173840200-173849600	Strong transcription	Placenta	Placenta
25	chr1:173840200-173854200	Weak transcription	Colonic Mucosa	Colon
26	chr1:173840200-173854800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:173840200-173856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:173840400-173845800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:173840400-173846400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:173840400-173846400	Weak transcription	Brain Germinal Matrix	brain
31	chr1:173840400-173846400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:173840400-173855000	Weak transcription	Psoas Muscle	Psoas
33	chr1:173840600-173849400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:173840600-173854200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:173840800-173846600	Weak transcription	Fetal Thymus	thymus
36	chr1:173840800-173848400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:173840800-173854200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:173840800-173854200	Weak transcription	Brain Anterior Caudate	brain
39	chr1:173840800-173854200	Weak transcription	NHLF	lung
40	chr1:173840800-173854600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:173840800-173854600	Weak transcription	Hela-S3	cervix
42	chr1:173840800-173854800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:173840800-173854800	Weak transcription	Brain Angular Gyrus	brain
44	chr1:173840800-173855000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:173840800-173855000	Weak transcription	NHDF-Ad	bronchial
46	chr1:173841000-173846000	Weak transcription	HepG2	liver
47	chr1:173841000-173846000	Weak transcription	NH-A	brain
48	chr1:173841000-173847000	Weak transcription	HUVEC	blood vessel
49	chr1:173841000-173854800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:173841000-173854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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