Variant report

Variant	rs16866420
Chromosome Location	chr2:179491235-179491236
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179489348..179492124-chr2:179493516..179496969,5	K562	blood:
2	chr2:179356121..179358654-chr2:179491189..179492895,2	K562	blood:
3	chr2:179490234..179492399-chr2:179495010..179497481,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1001238	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12052983	0.81[CHB][hapmap]
rs12693162	0.94[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12988307	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1560221	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16866342	0.85[CHB][hapmap]
rs16866400	1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.87[ASN][1000 genomes]
rs16866418	0.82[TSI][hapmap]
rs1978580	0.81[CHB][hapmap]
rs2042995	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2042996	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2163009	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288571	0.81[JPT][hapmap]
rs2303537	0.81[CHB][hapmap]
rs2303828	0.85[TSI][hapmap]
rs2303838	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs2366751	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2472751	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2562830	0.82[TSI][hapmap]
rs2562834	0.82[TSI][hapmap]
rs2562838	0.82[TSI][hapmap]
rs2562839	0.82[TSI][hapmap]
rs2562845	0.94[TSI][hapmap]
rs2562848	0.82[MKK][hapmap]
rs2627038	0.81[MKK][hapmap]
rs2627043	0.82[TSI][hapmap]
rs2742327	0.82[TSI][hapmap]
rs2742351	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs35504893	0.81[ASN][1000 genomes]
rs36113194	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731746	0.81[JPT][hapmap]
rs3731750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731754	0.85[CHB][hapmap]
rs3769864	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769866	0.86[CHB][hapmap]
rs3813250	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3820978	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3829746	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894029	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4894030	0.90[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs6704545	0.86[CHB][hapmap]
rs6712785	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6735077	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6753709	0.82[CHB][hapmap]
rs7600176	0.82[CHB][hapmap]
rs8179648	0.85[JPT][hapmap]
rs890578	0.81[JPT][hapmap]
rs957875	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs967507	0.86[CHB][hapmap]
rs9808377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1000642	chr2:179438866-179503211	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3394121	chr2:179491221-179491743	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16866420	TCOF1	trans	parietal	SCAN
rs16866420	HOXD9	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:179408000-179503000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:179438400-179518200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:179440600-179494000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:179440600-179505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:179441400-179498800	Weak transcription	Brain Anterior Caudate	brain
7	chr2:179441600-179495000	Weak transcription	Fetal Intestine Small	intestine
8	chr2:179442800-179492000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:179442800-179493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:179463800-179492000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:179464600-179497400	Weak transcription	GM12878-XiMat	blood
12	chr2:179472400-179502600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:179472800-179498600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:179473200-179498000	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:179473800-179491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:179477000-179502400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:179477200-179492400	Weak transcription	HSMM	muscle
18	chr2:179479000-179497400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:179479000-179500600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:179479600-179519400	Weak transcription	Fetal Thymus	thymus
21	chr2:179479800-179512000	Weak transcription	Lung	lung
22	chr2:179480400-179500600	Weak transcription	Ovary	ovary
23	chr2:179481400-179520000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:179482800-179500600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:179483200-179494200	Weak transcription	Pancreas	Pancrea
26	chr2:179483200-179655400	Weak transcription	Adipose Nuclei	Adipose
27	chr2:179483400-179495200	Weak transcription	Fetal Intestine Large	intestine
28	chr2:179483600-179496800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:179485400-179496800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:179486400-179495200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:179486400-179495200	Weak transcription	Right Ventricle	heart
32	chr2:179486600-179497200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:179486800-179498400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:179488400-179492600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:179488400-179492800	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:179489400-179493200	Weak transcription	Primary B cells from cord blood	blood
37	chr2:179489400-179494000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:179489600-179492800	Weak transcription	Primary T cells from cord blood	blood
39	chr2:179489600-179493400	Weak transcription	Left Ventricle	heart
40	chr2:179489600-179494000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:179489600-179497000	Weak transcription	Psoas Muscle	Psoas
42	chr2:179490000-179492600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:179490200-179492600	Weak transcription	HSMMtube	muscle
44	chr2:179490400-179492800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:179490800-179493000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr2:179491000-179491600	Active TSS	Fetal Muscle Trunk	muscle
47	chr2:179491000-179494400	Active TSS	Fetal Muscle Leg	muscle
48	chr2:179491000-179494400	Active TSS	Right Atrium	heart
49	chr2:179491200-179491400	Flanking Active TSS	Fetal Heart	heart

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