Variant report

Variant	rs240217
Chromosome Location	chr6:80713266-80713267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:80713261-80714856	GM19099	blood:	n/a	n/a
2	WRNIP1	chr6:80713199-80714075	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:80713036-80715077	GM12878	blood:	n/a	n/a
4	E2F4	chr6:80713236-80716364	MCF10A-Er-Src	breast:	n/a	chr6:80713962-80713969 chr6:80715312-80715321 chr6:80713962-80713969 chr6:80714200-80714210 chr6:80713962-80713969 chr6:80715314-80715323
5	JUN	chr6:80713167-80713331	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:80713220-80714622	H1-neurons	neurons:	n/a	n/a
7	REST	chr6:80713263-80714702	H1-neurons	neurons:	n/a	chr6:80714043-80714056 chr6:80714046-80714059
8	POLR2A	chr6:80713253-80713512	GM12878	blood:	n/a	n/a
9	RELA	chr6:80713213-80714934	GM15510	blood:	n/a	chr6:80714142-80714151 chr6:80714142-80714151
10	MXI1	chr6:80713176-80715124	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr6:80713208-80715469	GM12891	blood:	n/a	n/a
12	POLR2A	chr6:80713255-80715024	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80656144..80658220-chr6:80712686..80714230,2	K562	blood:

Variant related genes	Relation type
TTK	TF binding region
ENSG00000118402	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10943681	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10943682	0.93[ASN][1000 genomes]
rs10943688	0.95[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1205578	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1205579	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs12526265	0.96[ASN][1000 genomes]
rs1410521	0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1410522	0.95[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs151583	0.82[EUR][1000 genomes]
rs151587	0.81[EUR][1000 genomes]
rs151641	0.82[EUR][1000 genomes]
rs151642	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs151644	0.82[EUR][1000 genomes]
rs151645	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs151648	0.81[EUR][1000 genomes]
rs151654	0.82[EUR][1000 genomes]
rs151656	0.82[EUR][1000 genomes]
rs151657	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151658	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs151660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151663	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs151664	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs151665	0.81[EUR][1000 genomes]
rs181177	0.81[EUR][1000 genomes]
rs1897870	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1927425	0.91[CHB][hapmap]
rs1927426	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2181070	0.93[ASN][1000 genomes]
rs2295838	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2295840	0.95[ASN][1000 genomes]
rs2295841	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs239495	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs239496	0.83[EUR][1000 genomes]
rs239497	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs239500	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239501	0.82[EUR][1000 genomes]
rs239502	0.82[EUR][1000 genomes]
rs239515	0.81[EUR][1000 genomes]
rs239552	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs239553	0.82[EUR][1000 genomes]
rs239554	0.85[CEU][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs239555	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs239558	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs239560	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239562	0.82[EUR][1000 genomes]
rs239563	0.82[EUR][1000 genomes]
rs239566	0.82[EUR][1000 genomes]
rs239567	0.82[EUR][1000 genomes]
rs239568	0.82[EUR][1000 genomes]
rs239569	0.81[EUR][1000 genomes]
rs239570	0.81[EUR][1000 genomes]
rs239571	0.81[EUR][1000 genomes]
rs239572	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs239573	0.83[EUR][1000 genomes]
rs239574	0.82[EUR][1000 genomes]
rs239577	0.81[EUR][1000 genomes]
rs239578	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239579	0.81[EUR][1000 genomes]
rs239580	0.81[EUR][1000 genomes]
rs239581	0.80[EUR][1000 genomes]
rs239582	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs239583	0.93[JPT][hapmap]
rs239587	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs239589	0.85[CEU][hapmap]
rs240212	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs240213	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs240214	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240216	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs240218	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240225	0.82[EUR][1000 genomes]
rs240226	0.82[EUR][1000 genomes]
rs240228	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs240229	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs240237	0.82[EUR][1000 genomes]
rs2757084	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2769337	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3799497	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3812151	0.83[ASN][1000 genomes]
rs3828761	0.81[EUR][1000 genomes]
rs402128	0.82[EUR][1000 genomes]
rs465480	0.81[EUR][1000 genomes]
rs465483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706108	0.83[ASN][1000 genomes]
rs4706826	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4706827	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs587984	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61794	0.85[CEU][hapmap]
rs61795	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs61796	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs652752	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653665	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs666040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6923330	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs6925415	0.85[ASN][1000 genomes]
rs9294168	0.93[ASN][1000 genomes]
rs9341801	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9341802	0.93[ASN][1000 genomes]
rs9341803	0.92[ASN][1000 genomes]
rs9343961	0.92[ASN][1000 genomes]
rs9343965	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs9352790	0.93[ASN][1000 genomes]
rs9352797	0.83[ASN][1000 genomes]
rs9359406	0.92[ASN][1000 genomes]
rs9448877	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9448881	0.87[TSI][hapmap]

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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs240217	HTR1B	cis	parietal	SCAN
rs240217	ELOVL4	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80712600-80713400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:80712600-80713400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:80712600-80713600	Enhancers	Esophagus	oesophagus
4	chr6:80712600-80713600	Enhancers	Small Intestine	intestine
5	chr6:80712600-80714000	Flanking Active TSS	Dnd41	blood
6	chr6:80712600-80714600	Active TSS	Rectal Smooth Muscle	rectum
7	chr6:80713000-80713400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr6:80713000-80713400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:80713000-80713400	Flanking Active TSS	Thymus	Thymus
10	chr6:80713000-80713400	Flanking Active TSS	HepG2	liver
11	chr6:80713000-80713600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:80713000-80713600	Enhancers	Stomach Mucosa	stomach
13	chr6:80713000-80714000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr6:80713000-80714600	Active TSS	Brain Angular Gyrus	brain
15	chr6:80713200-80713400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr6:80713200-80713400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:80713200-80713400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:80713200-80713400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:80713200-80713400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr6:80713200-80713400	Bivalent/Poised TSS	Primary B cells from cord blood	blood
21	chr6:80713200-80713400	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:80713200-80713400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:80713200-80713400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:80713200-80713400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr6:80713200-80713400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:80713200-80713400	Active TSS	Brain Cingulate Gyrus	brain
27	chr6:80713200-80713400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:80713200-80713400	Enhancers	Colonic Mucosa	Colon
29	chr6:80713200-80713400	Enhancers	Colon Smooth Muscle	Colon
30	chr6:80713200-80713400	Active TSS	Duodenum Mucosa	Duodenum
31	chr6:80713200-80713400	Flanking Active TSS	Fetal Brain Male	brain
32	chr6:80713200-80713400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr6:80713200-80713400	Enhancers	Fetal Muscle Trunk	muscle
34	chr6:80713200-80713400	Enhancers	Fetal Muscle Leg	muscle
35	chr6:80713200-80713400	Enhancers	Pancreas	Pancrea
36	chr6:80713200-80713400	Enhancers	Psoas Muscle	Psoas
37	chr6:80713200-80713400	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr6:80713200-80713400	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr6:80713200-80713400	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr6:80713200-80713400	Enhancers	Hela-S3	cervix
41	chr6:80713200-80713400	Enhancers	HMEC	breast
42	chr6:80713200-80713400	Enhancers	HUVEC	blood vessel
43	chr6:80713200-80713600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr6:80713200-80713600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
45	chr6:80713200-80713600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:80713200-80713600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:80713200-80713600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:80713200-80713600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:80713200-80713600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr6:80713200-80713600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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