Variant report

Variant	rs17021217
Chromosome Location	chr4:147114344-147114345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147113098..147115033-chr4:147118947..147121819,2	K562	blood:
2	chr4:147106019..147107613-chr4:147111595..147114491,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10000407	0.83[EUR][1000 genomes]
rs10017509	0.83[CEU][hapmap]
rs10519776	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722991	0.83[CEU][hapmap]
rs11723069	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.85[EUR][1000 genomes]
rs11725678	0.81[EUR][1000 genomes]
rs11728525	0.85[EUR][1000 genomes]
rs11728609	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734320	0.83[CEU][hapmap]
rs11940961	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[EUR][1000 genomes]
rs12152657	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186313	0.81[CEU][hapmap]
rs17021186	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021239	0.82[CEU][hapmap]
rs17021241	0.83[CEU][hapmap]
rs17756056	0.82[EUR][1000 genomes]
rs17756234	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757715	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864371	0.88[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs1865531	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007366	0.83[EUR][1000 genomes]
rs2068009	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393640	0.81[EUR][1000 genomes]
rs28420466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733461	0.83[CEU][hapmap]
rs3756081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948408	0.81[EUR][1000 genomes]
rs4282199	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549398	0.81[EUR][1000 genomes]
rs4835283	0.81[CEU][hapmap]
rs4835284	0.83[CEU][hapmap]
rs4835286	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs55736910	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.85[EUR][1000 genomes]
rs56279747	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289966	0.81[EUR][1000 genomes]
rs56333123	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.98[ASN][1000 genomes]
rs62326764	0.81[EUR][1000 genomes]
rs62326797	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326802	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326804	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537399	0.81[EUR][1000 genomes]
rs6537400	0.83[EUR][1000 genomes]
rs6537401	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813969	0.82[CEU][hapmap]
rs6815527	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832576	0.83[EUR][1000 genomes]
rs6838174	0.85[CEU][hapmap]
rs6838458	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843421	0.82[CEU][hapmap]
rs6844381	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727922	0.81[EUR][1000 genomes]
rs72727944	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.98[ASN][1000 genomes]
rs7657269	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665079	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695415	0.83[EUR][1000 genomes]
rs7745	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308199	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17021217	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs17021217	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs17021217	RP11-6L6.2	cis	lung	GTEx
rs17021217	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147097800-147115400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:147098400-147118600	Weak transcription	Colonic Mucosa	Colon
3	chr4:147101400-147116200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:147103800-147117400	Strong transcription	Primary T cells from cord blood	blood
5	chr4:147109000-147116800	Weak transcription	Brain Substantia Nigra	brain
6	chr4:147109000-147123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:147109800-147116800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:147109800-147126000	Weak transcription	Aorta	Aorta
9	chr4:147110000-147115400	Weak transcription	Fetal Kidney	kidney
10	chr4:147110000-147116600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:147110400-147115600	Weak transcription	Brain Angular Gyrus	brain
12	chr4:147110400-147116800	Weak transcription	Esophagus	oesophagus
13	chr4:147111400-147114400	Strong transcription	GM12878-XiMat	blood
14	chr4:147111800-147115400	Weak transcription	Fetal Brain Female	brain
15	chr4:147111800-147116200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:147111800-147117000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:147112000-147117000	Weak transcription	Ovary	ovary
18	chr4:147112000-147127200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:147112200-147114600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:147112200-147115000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:147112200-147115400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:147112200-147116200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:147112200-147116800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:147112200-147117000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:147112200-147118400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:147112200-147124800	Weak transcription	Spleen	Spleen
27	chr4:147112200-147125200	Weak transcription	Pancreas	Pancrea
28	chr4:147112400-147115800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:147112400-147116800	Weak transcription	Dnd41	blood
30	chr4:147112800-147114400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:147112800-147114800	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:147112800-147116000	Weak transcription	NH-A	brain
33	chr4:147112800-147117000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:147112800-147127600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:147113000-147114600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:147113000-147114600	Weak transcription	A549	lung
37	chr4:147113000-147115200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:147113000-147115400	Weak transcription	K562	blood
39	chr4:147113000-147116600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:147113000-147117000	Weak transcription	HSMMtube	muscle
41	chr4:147113200-147114800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:147113200-147114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:147113200-147115400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:147113200-147123000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:147113200-147124200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:147113400-147115200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr4:147113400-147115400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:147113400-147115600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr4:147113400-147124400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:147113600-147114800	Weak transcription	NHLF	lung

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