Variant report

Variant	rs6679
Chromosome Location	chr1:113243048-113243049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:168)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:168 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113242406-113244648	GM12891	blood:	n/a	n/a
2	KAP1	chr1:113242881-113244059	U2OS	brain:	n/a	chr1:113243474-113243482
3	HCFC1	chr1:113242919-113243821	K562	blood:	n/a	n/a
4	RCOR1	chr1:113242988-113243927	K562	blood:	n/a	n/a
5	ZBTB7A	chr1:113242993-113243757	K562	blood:	n/a	n/a
6	TCF12	chr1:113243039-113243988	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr1:113240102-113248907	U87	brain:	n/a	n/a
8	POLR2A	chr1:113242991-113245744	HepG2	liver:	n/a	n/a
9	MAFK	chr1:113243007-113243969	K562	blood:	n/a	n/a
10	CBX3	chr1:113242817-113243845	K562	blood:	n/a	n/a
11	POLR2A	chr1:113242791-113245242	GM18505	blood:	n/a	n/a
12	POLR2A	chr1:113242543-113244402	MCF10A-Er-Src	breast:	n/a	n/a
13	SP1	chr1:113242970-113243896	K562	blood:	n/a	chr1:113243480-113243494 chr1:113243480-113243489 chr1:113243424-113243435
14	POLR2A	chr1:113242765-113246490	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:113242508-113244928	Hela-S3	cervix:	n/a	n/a
16	NR3C1	chr1:113242779-113243245	A549	lung:	n/a	n/a
17	POLR2A	chr1:113242979-113243225	HepG2	liver:	n/a	n/a
18	ELF1	chr1:113242995-113243716	K562	blood:	n/a	n/a
19	POLR2A	chr1:113242995-113245745	HCT-116	colon:	n/a	n/a
20	NFIC	chr1:113242943-113244021	ECC-1	luminal epithelium:	n/a	chr1:113243588-113243604 chr1:113243588-113243605
21	NFATC1	chr1:113243028-113243974	GM12878	blood:	n/a	n/a
22	ZNF143	chr1:113243040-113243966	K562	blood:	n/a	n/a
23	EGR1	chr1:113243003-113243726	K562	blood:	n/a	n/a
24	TAF1	chr1:113242951-113243861	K562	blood:	n/a	n/a
25	ZC3H11A	chr1:113242930-113243708	K562	blood:	n/a	n/a
26	BCL3	chr1:113242793-113245886	A549	lung:	n/a	n/a
27	KAP1	chr1:113242878-113243979	HEK293	kidney:	n/a	chr1:113243474-113243482
28	JUND	chr1:113243020-113244301	HCT-116	colon:	n/a	n/a
29	POLR2A	chr1:113242402-113245857	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr1:113240738-113245862	K562	blood:	n/a	n/a
31	MEF2A	chr1:113242985-113243722	K562	blood:	n/a	n/a
32	POLR2A	chr1:113240207-113248892	K562	blood:	n/a	n/a
33	JUND	chr1:113242902-113244410	A549	lung:	n/a	n/a
34	POLR2A	chr1:113241110-113248218	K562	blood:	n/a	n/a
35	POLR2A	chr1:113243035-113243270	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:113240680-113249021	K562	blood:	n/a	n/a
37	CEBPD	chr1:113242955-113243906	K562	blood:	n/a	n/a
38	ELF1	chr1:113242998-113243748	GM12878	blood:	n/a	n/a
39	CEBPB	chr1:113243017-113243885	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:113242885-113244634	GM19193	blood:	n/a	n/a
41	CHD2	chr1:113242644-113243920	K562	blood:	n/a	n/a
42	POLR2A	chr1:113242915-113248528	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:113243040-113243190	Gliobla	brain:	n/a	n/a
44	POLR2A	chr1:113242313-113244687	K562	blood:	n/a	n/a
45	UBTF	chr1:113242818-113244069	K562	blood:	n/a	n/a
46	JUND	chr1:113242713-113244698	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr1:113241223-113246166	K562	blood:	n/a	n/a
48	HEY1	chr1:113242133-113244405	K562	blood:	n/a	n/a
49	EP300	chr1:113242834-113243892	K562	blood:	n/a	n/a
50	REST	chr1:113243017-113243651	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113242660..113244199-chr17:59477359..59479903,2	MCF-7	breast:
2	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
3	chr1:113160443..113165363-chr1:113242054..113245654,5	K562	blood:
4	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
5	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
6	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
7	chr1:112937481..112939065-chr1:113242426..113245199,2	MCF-7	breast:
8	chr1:113240296..113243095-chr1:113496225..113498995,2	K562	blood:
9	chr1:113184100..113185954-chr1:113242899..113245081,2	K562	blood:
10	chr1:113215224..113219998-chr1:113238829..113244717,20	MCF-7	breast:
11	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
12	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225075	TF binding region
ENSG00000235299	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000271810	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1106287	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1110042	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102513	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11102514	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11102520	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12030612	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12030641	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12040988	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12049572	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12120956	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12122980	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12126684	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12126971	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12130243	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12133583	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12137269	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs12406282	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12728311	0.84[EUR][1000 genomes]
rs12756815	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17030613	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17030651	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2009056	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2273368	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs2279499	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2306937	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2306940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2887882	0.87[EUR][1000 genomes]
rs34848593	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3737136	0.94[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs3748656	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795819	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61818802	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61818805	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883593	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9308256	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv997362	chr1:113234820-113243297	Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6679	GSTM2	cis	parietal	SCAN
rs6679	SLC16A4	cis	cerebellum	SCAN
rs6679	WNT2B	cis	parietal	SCAN
rs6679	AMPD1	cis	cerebellum	SCAN
rs6679	ST7L	cis	lymphoblastoid	seeQTL
rs6679	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs6679	CAPZA1	cis	cerebellum	SCAN
rs6679	SYT6	cis	parietal	SCAN
rs6679	ST7L	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
2	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:113229600-113243200	Strong transcription	Dnd41	blood
4	chr1:113230200-113243200	Strong transcription	Primary T cells from cord blood	blood
5	chr1:113231600-113243200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:113234000-113244400	Strong transcription	Thymus	Thymus
7	chr1:113235800-113244600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:113237200-113243400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:113237200-113243400	Strong transcription	Brain Germinal Matrix	brain
10	chr1:113238000-113246400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:113238400-113243200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:113238400-113243600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:113238800-113246600	Genic enhancers	Placenta Amnion	Placenta Amnion
14	chr1:113239400-113246600	Genic enhancers	Fetal Intestine Large	intestine
15	chr1:113240200-113243800	Enhancers	Fetal Heart	heart
16	chr1:113240400-113247000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr1:113240400-113247200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:113240600-113243200	Genic enhancers	H1 Cell Line	embryonic stem cell
19	chr1:113240600-113243200	Genic enhancers	HSMMtube	muscle
20	chr1:113240600-113244600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:113240600-113245600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:113240600-113245800	Genic enhancers	Lung	lung
23	chr1:113240600-113246800	Genic enhancers	Colonic Mucosa	Colon
24	chr1:113240600-113247000	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr1:113240600-113247000	Genic enhancers	Fetal Muscle Leg	muscle
26	chr1:113240600-113247200	Genic enhancers	Placenta	Placenta
27	chr1:113240800-113243400	Enhancers	Right Atrium	heart
28	chr1:113240800-113244400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
29	chr1:113240800-113244600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
30	chr1:113240800-113246400	Genic enhancers	Pancreas	Pancrea
31	chr1:113240800-113246600	Genic enhancers	Adipose Nuclei	Adipose
32	chr1:113240800-113247200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:113241000-113245800	Genic enhancers	Gastric	stomach
34	chr1:113241000-113246600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:113241200-113243200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:113241200-113243800	Enhancers	Right Ventricle	heart
37	chr1:113241200-113243800	Enhancers	Stomach Mucosa	stomach
38	chr1:113241200-113244200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:113241200-113244600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:113241200-113244800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:113241200-113247000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
42	chr1:113241200-113247200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:113241400-113243200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:113241400-113246400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:113241400-113246600	Genic enhancers	HMEC	breast
46	chr1:113241600-113247000	Genic enhancers	Fetal Intestine Small	intestine
47	chr1:113241600-113249200	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:113241800-113243400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:113241800-113247000	Genic enhancers	Colon Smooth Muscle	Colon
50	chr1:113242000-113243400	Genic enhancers	NHEK	skin

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