Variant report

Variant	rs9374432
Chromosome Location	chr6:114316404-114316405
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	CTCF	chr6:114316027-114316441	K562	blood:	n/a	chr6:114316233-114316251
2	KAP1	chr6:114315989-114316579	HEK293	kidney:	n/a	n/a
3	CBX3	chr6:114315847-114316565	HCT-116	colon:	n/a	n/a
4	RAD21	chr6:114315969-114316444	Hela-S3	cervix:	n/a	chr6:114316234-114316253
5	NFIC	chr6:114316002-114316508	ECC-1	luminal epithelium:	n/a	n/a
6	YY1	chr6:114315971-114316498	ECC-1	luminal epithelium:	n/a	chr6:114316138-114316154
7	RAD21	chr6:114315834-114316506	MCF-7	breast:	n/a	chr6:114316234-114316253
8	SMC3	chr6:114315971-114316453	Hela-S3	cervix:	n/a	chr6:114316235-114316243 chr6:114316235-114316249
9	RAD21	chr6:114315779-114316681	HCT-116	colon:	n/a	chr6:114316234-114316253
10	BACH1	chr6:114316068-114316405	H1-hESC	embryonic stem cell:	n/a	n/a
11	YY1	chr6:114315965-114316479	SK-N-SH	brain:	n/a	chr6:114316138-114316154
12	CTCF	chr6:114315870-114316461	MCF-7	breast:	n/a	chr6:114316233-114316251
13	YY1	chr6:114315992-114316415	SK-N-SH_RA	brain:	n/a	chr6:114316138-114316154
14	CTCF	chr6:114315837-114316671	SK-N-SH	brain:	n/a	chr6:114316233-114316251
15	MYC	chr6:114315980-114316425	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr6:114315853-114316527	A549	lung:	n/a	chr6:114316234-114316253
17	RAD21	chr6:114315888-114317185	IMR90	lung:	n/a	chr6:114316234-114316253
18	CTCF	chr6:114315924-114316416	A549	lung:	n/a	chr6:114316233-114316251
19	YY1	chr6:114315995-114316425	H1-hESC	embryonic stem cell:	n/a	chr6:114316138-114316154
20	TCF12	chr6:114315883-114317288	ECC-1	luminal epithelium:	n/a	chr6:114317088-114317095 chr6:114316293-114316300 chr6:114317086-114317093
21	TEAD4	chr6:114315918-114316466	HepG2	liver:	n/a	n/a
22	SIN3A	chr6:114316036-114316442	H1-hESC	embryonic stem cell:	n/a	n/a
23	FOXA2	chr6:114316093-114316427	HepG2	liver:	n/a	n/a
24	MAX	chr6:114315997-114316520	ECC-1	luminal epithelium:	n/a	n/a
25	TCF12	chr6:114316027-114317343	SK-N-SH	brain:	n/a	chr6:114317088-114317095 chr6:114316293-114316300 chr6:114317086-114317093
26	RAD21	chr6:114316001-114316434	SK-N-SH_RA	brain:	n/a	chr6:114316234-114316253
27	RAD21	chr6:114315885-114316526	H1-hESC	embryonic stem cell:	n/a	chr6:114316234-114316253
28	RAD21	chr6:114315868-114316535	MCF-7	breast:	n/a	chr6:114316234-114316253
29	TEAD4	chr6:114315918-114316603	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr6:114315967-114316410	PANC-1	pancreas:	n/a	n/a
31	YY1	chr6:114316067-114316405	HepG2	liver:	n/a	chr6:114316138-114316154
32	YY1	chr6:114316047-114316463	SK-N-SH_RA	brain:	n/a	chr6:114316138-114316154
33	JUND	chr6:114315988-114317208	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr6:114316072-114316423	MCF-7	breast:	n/a	n/a
35	TEAD4	chr6:114315923-114316535	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZNF143	chr6:114316014-114316413	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr6:114315991-114316451	IMR90	lung:	n/a	n/a
38	CTCF	chr6:114316028-114316406	K562	blood:	n/a	chr6:114316233-114316251
39	TCF12	chr6:114316009-114316466	ECC-1	luminal epithelium:	n/a	chr6:114316293-114316300
40	CTCF	chr6:114315970-114316424	GM12878	blood:	n/a	chr6:114316233-114316251
41	SMC3	chr6:114315990-114316458	HepG2	liver:	n/a	chr6:114316235-114316243 chr6:114316235-114316249
42	CTCF	chr6:114315958-114316407	A549	lung:	n/a	chr6:114316233-114316251
43	CTCF	chr6:114315912-114316628	HCT-116	colon:	n/a	chr6:114316233-114316251
44	CTCF	chr6:114315818-114316610	A549	lung:	n/a	chr6:114316233-114316251
45	TEAD4	chr6:114316055-114316460	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr6:114315885-114316610	HCT-116	colon:	n/a	chr6:114316234-114316253
47	RAD21	chr6:114315937-114316436	HepG2	liver:	n/a	chr6:114316234-114316253
48	STAT3	chr6:114316105-114316708	MCF10A-Er-Src	breast:	n/a	n/a
49	PBX3	chr6:114315885-114316561	SK-N-SH	brain:	n/a	chr6:114316256-114316265
50	CTCF	chr6:114315682-114317318	HCT-116	colon:	n/a	chr6:114316233-114316251

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MARCKS-5	chr6:114316308-114316415	ENSG00000228624

Variant related genes	Relation type
ENSG00000228624	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1157989	0.80[CEU][hapmap]
rs11967410	0.81[CEU][hapmap]
rs12190983	0.81[CEU][hapmap]
rs12211751	0.81[CEU][hapmap]
rs2475617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475618	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2475619	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475621	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475622	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2475623	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2475624	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2475625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2475626	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475628	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2499610	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2499611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499612	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2499613	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499616	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2499620	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002601	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4296916	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4296917	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4551200	1.00[CEU][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]
rs4945985	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6568821	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6568824	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7743208	0.81[CEU][hapmap]
rs7764690	0.90[CEU][hapmap]
rs9320476	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9320477	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9320479	0.81[CEU][hapmap]
rs9398370	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488300	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9488301	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9488302	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9488303	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9488304	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114309400-114318600	Weak transcription	Right Atrium	heart
2	chr6:114311600-114317000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:114311600-114317000	Weak transcription	Placenta	Placenta
4	chr6:114311800-114332400	Weak transcription	Fetal Brain Female	brain
5	chr6:114314600-114331200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:114315400-114316800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:114315400-114317200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:114315800-114316800	Enhancers	Hela-S3	cervix
9	chr6:114315800-114317200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:114315800-114317200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr6:114315800-114317200	Enhancers	HSMM	muscle
12	chr6:114315800-114317800	Enhancers	Dnd41	blood
13	chr6:114315800-114318600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:114316000-114316600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr6:114316000-114317200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr6:114316000-114317400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr6:114316000-114318400	Enhancers	Fetal Muscle Leg	muscle
18	chr6:114316200-114316600	Enhancers	Brain Cingulate Gyrus	brain
19	chr6:114316200-114316800	Enhancers	Colon Smooth Muscle	Colon
20	chr6:114316200-114316800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:114316200-114317000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:114316200-114317000	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr6:114316200-114317200	Enhancers	H9 Cell Line	embryonic stem cell
24	chr6:114316200-114317200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:114316200-114317200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:114316200-114317200	Enhancers	Brain Germinal Matrix	brain
27	chr6:114316200-114317200	Enhancers	Fetal Intestine Large	intestine
28	chr6:114316200-114317200	Enhancers	Fetal Intestine Small	intestine
29	chr6:114316200-114317200	Enhancers	Fetal Lung	lung
30	chr6:114316200-114317200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:114316200-114317200	Enhancers	HepG2	liver
32	chr6:114316200-114317400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:114316200-114317400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:114316200-114317600	Enhancers	Fetal Heart	heart
35	chr6:114316200-114317800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:114316200-114317800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:114316200-114317800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:114316200-114317800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:114316200-114318000	Enhancers	NH-A	brain
40	chr6:114316200-114318400	Enhancers	Adipose Nuclei	Adipose
41	chr6:114316200-114318800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:114316200-114318800	Enhancers	Rectal Smooth Muscle	rectum
43	chr6:114316200-114318800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr6:114316200-114318800	Enhancers	Stomach Smooth Muscle	stomach
45	chr6:114316200-114318800	Enhancers	HMEC	breast
46	chr6:114316200-114319000	Enhancers	NHEK	skin
47	chr6:114316200-114319200	Enhancers	NHLF	lung
48	chr6:114316200-114319200	Enhancers	Osteobl	bone
49	chr6:114316200-114320000	Enhancers	HUVEC	blood vessel
50	chr6:114316400-114316800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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