Variant report

Variant	rs8008094
Chromosome Location	chr14:31090752-31090753
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	POLR2A	chr14:31090546-31090928	A549	lung:	n/a	n/a
2	CEBPB	chr14:31090721-31090960	HepG2	liver:	n/a	chr14:31090888-31090899 chr14:31090888-31090899 chr14:31090889-31090900
3	CCNT2	chr14:31090625-31091970	K562	blood:	n/a	chr14:31091729-31091738
4	POLR2A	chr14:31090434-31092076	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr14:31090243-31091996	MCF-7	breast:	n/a	chr14:31090438-31090446 chr14:31090435-31090444 chr14:31090433-31090446 chr14:31090435-31090444 chr14:31090434-31090445
6	USF2	chr14:31090693-31090884	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr14:31090610-31091907	K562	blood:	n/a	n/a
8	POLR2A	chr14:31090596-31090893	A549	lung:	n/a	n/a
9	GABPA	chr14:31090666-31091921	A549	lung:	n/a	n/a
10	POLR2A	chr14:31090633-31092158	HepG2	liver:	n/a	n/a
11	NR2F2	chr14:31090464-31092008	MCF-7	breast:	n/a	n/a
12	POLR2A	chr14:31090359-31092144	GM12878	blood:	n/a	n/a
13	POLR2A	chr14:31090392-31091954	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr14:31090525-31090921	GM12878	blood:	n/a	n/a
15	POLR2A	chr14:31090527-31091944	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr14:31090445-31092145	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr14:31090635-31092098	GM12878	blood:	n/a	n/a
18	MBD4	chr14:31090107-31092432	HepG2	liver:	n/a	n/a
19	POLR2A	chr14:31090556-31090955	SK-N-SH	brain:	n/a	n/a
20	ZNF143	chr14:31090674-31090796	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr14:31090363-31092065	GM12878	blood:	n/a	n/a
22	MTA3	chr14:31090324-31092061	GM12878	blood:	n/a	n/a
23	GATA3	chr14:31090227-31092177	MCF-7	breast:	n/a	chr14:31091901-31091908 chr14:31091901-31091908 chr14:31091897-31091913 chr14:31091901-31091908 chr14:31091894-31091915
24	RCOR1	chr14:31090648-31091584	K562	blood:	n/a	n/a
25	POLR2A	chr14:31090470-31092023	GM12891	blood:	n/a	n/a
26	POLR2A	chr14:31090488-31092093	HUVEC	blood vessel:	n/a	n/a
27	TCF12	chr14:31090529-31092054	A549	lung:	n/a	n/a
28	POLR2A	chr14:31090564-31090951	A549	lung:	n/a	n/a
29	POLR2A	chr14:31090321-31092018	GM18505	blood:	n/a	n/a
30	POLR2A	chr14:31090367-31092021	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr14:31090496-31092001	K562	blood:	n/a	n/a
32	POLR2A	chr14:31090449-31092032	GM12891	blood:	n/a	n/a
33	POLR2A	chr14:31090537-31090898	MCF-7	breast:	n/a	n/a
34	RCOR1	chr14:31090578-31091839	HepG2	liver:	n/a	n/a
35	POLR2A	chr14:31090464-31091948	HepG2	liver:	n/a	n/a
36	TAF1	chr14:31090525-31092001	MCF-7	breast:	n/a	n/a
37	POLR2A	chr14:31090663-31092003	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr14:31090323-31091871	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr14:31090538-31092149	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr14:31090528-31091927	HepG2	liver:	n/a	n/a
41	BCL3	chr14:31090258-31092000	A549	lung:	n/a	n/a
42	POLR2A	chr14:31090356-31091031	K562	blood:	n/a	n/a
43	YY1	chr14:31090495-31090842	K562	blood:	n/a	n/a
44	BCL3	chr14:31090411-31092048	A549	lung:	n/a	n/a
45	ATF2	chr14:31090487-31092090	GM12878	blood:	n/a	n/a
46	JUND	chr14:31090300-31091970	MCF-7	breast:	n/a	chr14:31091146-31091155 chr14:31091453-31091467 chr14:31091951-31091965
47	POLR2A	chr14:31090415-31092079	K562	blood:	n/a	n/a
48	RELA	chr14:31090702-31092026	GM10847	blood:	n/a	n/a
49	CEBPB	chr14:31090708-31091065	Hela-S3	cervix:	n/a	chr14:31090888-31090899 chr14:31090888-31090899 chr14:31090889-31090900
50	SPI1	chr14:31090682-31091122	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:31090296..31092019-chr14:31343870..31346650,2	K562	blood:
2	chr14:31090018..31093014-chr14:31887951..31890191,2	MCF-7	breast:
3	chr14:31090029..31096005-chr14:31342159..31346650,8	K562	blood:
4	chr14:31090421..31092379-chr14:31107832..31110754,2	MCF-7	breast:
5	chr14:31027121..31031753-chr14:31090278..31094067,6	K562	blood:
6	chr14:31060440..31063351-chr14:31089762..31092777,3	MCF-7	breast:
7	chr14:31074562..31083390-chr14:31084587..31093565,15	K562	blood:
8	chr14:31071248..31073927-chr14:31089916..31091588,2	MCF-7	breast:
9	chr14:31067708..31069634-chr14:31090291..31092583,3	MCF-7	breast:
10	chr14:31025231..31028884-chr14:31089510..31093231,4	MCF-7	breast:
11	chr14:31027330..31031100-chr14:31087785..31093139,9	MCF-7	breast:

Variant related genes	Relation type
SCFD1	TF binding region
ENSG00000092108	Chromatin interaction
ENSG00000092140	Chromatin interaction
ENSG00000250365	Chromatin interaction
ENSG00000129493	Chromatin interaction
ENSG00000100473	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10130830	0.81[CHB][hapmap]
rs10131166	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10141944	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10142331	0.81[CHB][hapmap]
rs10146357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10147257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10149966	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1113946	0.88[CEU][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap]
rs11156637	0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1123860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11622076	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11623154	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11625381	0.81[CHB][hapmap]
rs11627421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11628700	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11846071	0.81[EUR][1000 genomes]
rs11846293	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11846408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11846420	0.85[CHD][hapmap]
rs11851205	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12434151	0.81[CHB][hapmap]
rs12586678	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12882048	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12882931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12888568	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs12894186	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs142983	0.82[CEU][hapmap]
rs17096941	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17097023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17097160	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs172946	0.81[CHB][hapmap]
rs2038451	0.87[CEU][hapmap]
rs2057284	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070339	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs2070340	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2273520	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229144	0.81[CHB][hapmap]
rs229150	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs229152	0.81[CHB][hapmap]
rs229154	0.81[CHB][hapmap]
rs229155	0.85[CHD][hapmap]
rs229161	0.81[CHB][hapmap]
rs229190	0.81[CHB][hapmap]
rs229209	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs229211	0.81[CHB][hapmap]
rs229244	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs230340	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs230351	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs230364	0.81[CHB][hapmap]
rs230366	0.81[CHB][hapmap]
rs2378780	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs2378782	0.81[CHB][hapmap]
rs28567474	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34935871	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35069045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35389182	0.87[EUR][1000 genomes]
rs3736773	0.88[CEU][hapmap]
rs4430662	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs447853	0.82[MEX][hapmap]
rs61976741	0.84[EUR][1000 genomes]
rs6571356	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6571357	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6571361	0.81[CHB][hapmap]
rs7141333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7141624	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7144204	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs7147530	0.81[CHB][hapmap]
rs7149113	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7153509	0.81[CHB][hapmap]
rs7154847	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs7493549	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs8006314	0.81[CHB][hapmap]
rs8012494	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs8013017	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015536	1.00[CHB][hapmap]
rs8018993	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8019637	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9322864	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs9806111	0.81[CHB][hapmap];0.85[CHD][hapmap]

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	nsv564169	chr14:30819087-31541494	Strong transcription Genic enhancers ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1036419	chr14:30969616-31224226	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901581	chr14:30978745-31585289	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv564171	chr14:31068090-31149630	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8008094	SCFD1	cis	parietal	SCAN
rs8008094	G2E3	cis	parietal	SCAN
rs8008094	SCFD1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31069000-31090800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:31071400-31090800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:31085600-31090800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:31086800-31090800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:31087000-31090800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr14:31089600-31090800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:31089800-31090800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr14:31090200-31090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:31090200-31090800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr14:31090200-31090800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr14:31090200-31091200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr14:31090200-31091200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr14:31090200-31091200	Flanking Active TSS	GM12878-XiMat	blood
14	chr14:31090200-31091400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:31090200-31091400	Flanking Active TSS	Osteobl	bone
16	chr14:31090200-31092400	Active TSS	Duodenum Mucosa	Duodenum
17	chr14:31090200-31092400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr14:31090200-31092400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr14:31090200-31092400	Active TSS	Placenta	Placenta
20	chr14:31090200-31092400	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr14:31090200-31092600	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr14:31090200-31092800	Active TSS	Fetal Intestine Large	intestine
23	chr14:31090200-31092800	Active TSS	Psoas Muscle	Psoas
24	chr14:31090200-31093000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:31090200-31093200	Active TSS	Fetal Lung	lung
26	chr14:31090200-31093400	Active TSS	Fetal Brain Female	brain
27	chr14:31090200-31093400	Active TSS	Right Atrium	heart
28	chr14:31090200-31093600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr14:31090400-31090800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr14:31090400-31090800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr14:31090400-31090800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr14:31090400-31090800	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr14:31090400-31090800	Flanking Active TSS	HepG2	liver
34	chr14:31090400-31091000	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr14:31090400-31091000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr14:31090400-31091000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:31090400-31091000	Active TSS	Brain Germinal Matrix	brain
38	chr14:31090400-31091000	Flanking Active TSS	Fetal Muscle Leg	muscle
39	chr14:31090400-31091000	Flanking Active TSS	Dnd41	blood
40	chr14:31090400-31091000	Flanking Active TSS	HMEC	breast
41	chr14:31090400-31091200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr14:31090400-31091200	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr14:31090400-31091200	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr14:31090400-31091200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr14:31090400-31091200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr14:31090400-31091200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr14:31090400-31091200	Flanking Active TSS	Fetal Thymus	thymus
48	chr14:31090400-31091200	Flanking Active TSS	Hela-S3	cervix
49	chr14:31090400-31091400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr14:31090400-31091400	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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