Variant report

Variant	rs1897870
Chromosome Location	chr6:80720286-80720287
allele	A/G
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	RAD21	chr6:80720011-80720297	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr6:80720160-80720310	HEEpiC	esophagus:	n/a	chr6:80720204-80720222
3	CTCF	chr6:80720160-80720310	Caco-2	colon:	n/a	chr6:80720204-80720222
4	CTCF	chr6:80720160-80720310	HMEC	breast:	n/a	chr6:80720204-80720222
5	RAD21	chr6:80720084-80720342	HepG2	liver:	n/a	n/a
6	CTCF	chr6:80720140-80720290	GM12878	blood:	n/a	chr6:80720204-80720222
7	CTCF	chr6:80720121-80720307	MCF-7	breast:	n/a	chr6:80720204-80720222
8	CTCF	chr6:80720200-80720350	BE2_C	brain:	n/a	chr6:80720204-80720222
9	ZNF143	chr6:80720063-80720286	GM12878	blood:	n/a	n/a
10	CTCF	chr6:80720167-80720290	Hela-S3	cervix:	n/a	chr6:80720204-80720222
11	CTCF	chr6:80720200-80720350	HPF	lung:	n/a	chr6:80720204-80720222
12	STAT3	chr6:80720091-80720343	MCF10A-Er-Src	breast:	n/a	n/a
13	RAD21	chr6:80719996-80720433	MCF-7	breast:	n/a	n/a
14	RAD21	chr6:80720024-80720391	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr6:80720140-80720290	RPTEC	kidney:	n/a	chr6:80720204-80720222
16	RAD21	chr6:80720081-80720298	SK-N-SH_RA	brain:	n/a	n/a
17	CTCF	chr6:80720140-80720290	HMEC	breast:	n/a	chr6:80720204-80720222
18	CTCF	chr6:80720180-80720330	HepG2	liver:	n/a	chr6:80720204-80720222
19	CTCF	chr6:80720140-80720290	GM12875	blood:	n/a	chr6:80720204-80720222
20	CTCF	chr6:80720037-80720386	GM12878	blood:	n/a	chr6:80720204-80720222
21	RAD21	chr6:80720112-80720311	HepG2	liver:	n/a	n/a
22	RAD21	chr6:80720085-80720289	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr6:80720180-80720330	HFF-Myc	foreskin:	n/a	chr6:80720204-80720222
24	CTCF	chr6:80720180-80720330	BE2_C	brain:	n/a	chr6:80720204-80720222
25	RAD21	chr6:80720054-80720322	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr6:80720122-80720381	MCF-7	breast:	n/a	chr6:80720204-80720222
27	CTCF	chr6:80720149-80720299	MCF-7	breast:	n/a	chr6:80720204-80720222
28	RAD21	chr6:80719961-80720452	HCT-116	colon:	n/a	n/a
29	CTCF	chr6:80720160-80720310	HepG2	liver:	n/a	chr6:80720204-80720222

No.	Distal block	Cell Line	Cell type
1	chr6:80718444..80720486-chr6:80838754..80840605,2	K562	blood:
2	chr6:80719003..80721359-chr6:80737643..80739358,2	K562	blood:
3	chr6:80649918..80652477-chr6:80718505..80720470,2	K562	blood:

Variant related genes	Relation type
TTK	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10943681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10943682	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10943688	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1205578	0.94[ASN][1000 genomes]
rs1205579	0.83[JPT][hapmap]
rs12526265	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1410521	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1410522	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs151642	0.93[ASN][1000 genomes]
rs151645	0.83[ASN][1000 genomes]
rs151657	0.93[ASN][1000 genomes]
rs151658	0.83[JPT][hapmap]
rs151660	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs151663	0.83[JPT][hapmap]
rs151664	0.83[JPT][hapmap]
rs1927425	0.83[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1927426	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2149082	0.83[EUR][1000 genomes]
rs2181070	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295840	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2295841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239495	0.85[ASN][1000 genomes]
rs239497	0.92[ASN][1000 genomes]
rs239500	0.93[ASN][1000 genomes]
rs239552	0.83[JPT][hapmap]
rs239554	0.83[JPT][hapmap]
rs239555	0.83[JPT][hapmap]
rs239558	0.83[JPT][hapmap]
rs239560	0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs239572	0.83[JPT][hapmap]
rs239578	0.93[ASN][1000 genomes]
rs239582	0.85[JPT][hapmap]
rs239583	0.93[JPT][hapmap]
rs239587	0.83[JPT][hapmap]
rs240212	0.83[JPT][hapmap]
rs240213	0.92[JPT][hapmap]
rs240214	0.94[ASN][1000 genomes]
rs240216	0.83[JPT][hapmap]
rs240217	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs240218	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs240228	0.83[JPT][hapmap]
rs240229	0.83[JPT][hapmap]
rs2757084	0.93[ASN][1000 genomes]
rs2769337	0.94[ASN][1000 genomes]
rs3799497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812151	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3967160	0.81[EUR][1000 genomes]
rs465483	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4706108	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4706826	0.92[ASN][1000 genomes]
rs4706827	0.83[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs587984	0.94[ASN][1000 genomes]
rs61795	0.83[JPT][hapmap]
rs61796	0.83[JPT][hapmap]
rs652752	0.94[ASN][1000 genomes]
rs653665	0.83[JPT][hapmap]
rs666040	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6925415	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9294168	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9341801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9341802	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9341803	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9343961	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9343965	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9350843	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs9352790	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9352797	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9359406	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9448877	0.91[ASN][1000 genomes]
rs9448880	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv5370	chr6:80715351-80751740	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1897870	HTR1B	cis	parietal	SCAN
rs1897870	SNAP91	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80714800-80738800	Weak transcription	Small Intestine	intestine
2	chr6:80715000-80730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:80715000-80748000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:80715000-80752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:80715000-80752400	Weak transcription	Placenta	Placenta
6	chr6:80715200-80721200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:80715200-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:80715200-80727000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:80715200-80730800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:80715200-80734000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:80715200-80734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:80715200-80739200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:80715200-80749600	Weak transcription	Fetal Intestine Small	intestine
14	chr6:80715200-80752000	Weak transcription	Primary B cells from cord blood	blood
15	chr6:80715200-80752200	Weak transcription	Primary T cells from cord blood	blood
16	chr6:80715400-80721200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:80715400-80721200	Weak transcription	Fetal Kidney	kidney
18	chr6:80715400-80722600	Weak transcription	Fetal Intestine Large	intestine
19	chr6:80715400-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:80715400-80727000	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:80715400-80729400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:80715400-80742200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:80715400-80743200	Weak transcription	Brain Germinal Matrix	brain
24	chr6:80715400-80745400	Weak transcription	Fetal Lung	lung
25	chr6:80715400-80755000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:80715400-80756800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:80715600-80721200	Weak transcription	Osteobl	bone
28	chr6:80715600-80724600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:80715600-80725200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:80715600-80739200	Weak transcription	Fetal Stomach	stomach
31	chr6:80715600-80754400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:80715600-80763800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:80715800-80720800	Weak transcription	NHDF-Ad	bronchial
34	chr6:80715800-80733400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:80715800-80753600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:80715800-80753800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:80715800-80754400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:80716000-80723000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:80716000-80726000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:80716000-80728600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:80716000-80729400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:80716000-80739200	Weak transcription	NHEK	skin
43	chr6:80716000-80743600	Weak transcription	Fetal Heart	heart
44	chr6:80716200-80725200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:80716200-80727800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:80716200-80728000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:80716200-80754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:80716400-80720400	Weak transcription	Hela-S3	cervix
49	chr6:80716400-80727800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:80716800-80720400	Strong transcription	K562	blood

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