Variant report

Variant	rs9398370
Chromosome Location	chr6:114316856-114316857
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	CEBPB	chr6:114316824-114317190	IMR90	lung:	n/a	n/a
2	RAD21	chr6:114316843-114317256	SK-N-SH_RA	brain:	n/a	n/a
3	TEAD4	chr6:114316682-114317337	ECC-1	luminal epithelium:	n/a	n/a
4	RCOR1	chr6:114316802-114317237	Hela-S3	cervix:	n/a	n/a
5	TCF7L2	chr6:114316782-114317243	Hela-S3	cervix:	n/a	n/a
6	NFIC	chr6:114316644-114317383	SK-N-SH	brain:	n/a	n/a
7	MAX	chr6:114316835-114317209	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr6:114316802-114317247	H1-hESC	embryonic stem cell:	n/a	n/a
9	GATA3	chr6:114316771-114317323	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr6:114315888-114317185	IMR90	lung:	n/a	chr6:114316234-114316253
11	NFIC	chr6:114316799-114317362	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr6:114315883-114317288	ECC-1	luminal epithelium:	n/a	chr6:114317088-114317095 chr6:114316293-114316300 chr6:114317086-114317093
13	KAP1	chr6:114316817-114317254	HEK293	kidney:	n/a	n/a
14	TCF12	chr6:114316027-114317343	SK-N-SH	brain:	n/a	chr6:114317088-114317095 chr6:114316293-114316300 chr6:114317086-114317093
15	TCF12	chr6:114316656-114317293	ECC-1	luminal epithelium:	n/a	chr6:114317088-114317095 chr6:114317086-114317093
16	CHD2	chr6:114316742-114317247	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr6:114316841-114317290	SK-N-SH	brain:	n/a	n/a
18	USF2	chr6:114316730-114317176	Hela-S3	cervix:	n/a	chr6:114316901-114316912 chr6:114317038-114317054
19	RAD21	chr6:114316699-114317261	Hela-S3	cervix:	n/a	n/a
20	MEF2A	chr6:114316689-114317269	SK-N-SH	brain:	n/a	n/a
21	JUND	chr6:114315988-114317208	Hela-S3	cervix:	n/a	n/a
22	MAFK	chr6:114316810-114317263	Hela-S3	cervix:	n/a	n/a
23	FOSL2	chr6:114316775-114317278	SK-N-SH	brain:	n/a	n/a
24	RFX5	chr6:114316734-114317234	Hela-S3	cervix:	n/a	n/a
25	EP300	chr6:114316679-114317279	ECC-1	luminal epithelium:	n/a	n/a
26	SP1	chr6:114316760-114317242	A549	lung:	n/a	n/a
27	PBX3	chr6:114316652-114317348	SK-N-SH	brain:	n/a	n/a
28	RAD21	chr6:114316843-114317307	ECC-1	luminal epithelium:	n/a	n/a
29	STAT3	chr6:114316774-114317271	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr6:114316760-114316910	NHLF	lung:	n/a	n/a
31	CEBPB	chr6:114316789-114317234	Hela-S3	cervix:	n/a	n/a
32	JUN	chr6:114316765-114317234	Hela-S3	cervix:	n/a	n/a
33	FOXM1	chr6:114316622-114317347	ECC-1	luminal epithelium:	n/a	n/a
34	TEAD4	chr6:114316687-114317337	ECC-1	luminal epithelium:	n/a	n/a
35	PBX3	chr6:114316660-114317211	SK-N-SH	brain:	n/a	n/a
36	CTCF	chr6:114315682-114317318	HCT-116	colon:	n/a	chr6:114316233-114316251
37	EP300	chr6:114315860-114317365	ECC-1	luminal epithelium:	n/a	chr6:114316432-114316441
38	FOSL2	chr6:114316687-114317215	SK-N-SH	brain:	n/a	n/a
39	EP300	chr6:114316653-114317288	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr6:114316856-114317094	SK-N-SH	brain:	n/a	n/a
41	EP300	chr6:114316771-114317234	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr6:114316800-114316950	MCF-7	breast:	n/a	n/a
43	RCOR1	chr6:114316528-114317248	IMR90	lung:	n/a	n/a
44	TEAD4	chr6:114316778-114317285	SK-N-SH	brain:	n/a	n/a
45	KAP1	chr6:114316768-114317196	U2OS	brain:	n/a	n/a
46	RAD21	chr6:114315733-114317434	SK-N-SH	brain:	n/a	chr6:114316234-114316253
47	RAD21	chr6:114316823-114317236	H1-hESC	embryonic stem cell:	n/a	n/a
48	NFIC	chr6:114316678-114317331	ECC-1	luminal epithelium:	n/a	n/a
49	NFIC	chr6:114316747-114317344	ECC-1	luminal epithelium:	n/a	n/a
50	TCF12	chr6:114316701-114317246	A549	lung:	n/a	chr6:114317088-114317095 chr6:114317086-114317093

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MARCKS-5	chr6:114316764-114317224	ENSG00000228624
2	lnc-MARCKS-5	chr6:114316764-114317079	ENSG00000228624
3	lnc-MARCKS-5	chr6:114316764-114317033	ENSG00000228624
4	lnc-MARCKS-5	chr6:114316764-114316966	ENSG00000228624
5	lnc-MARCKS-5	chr6:114316764-114316979	ENSG00000228624
6	lnc-MARCKS-5	chr6:114316764-114317224	ENSG00000228624
7	lnc-MARCKS-5	chr6:114316764-114317214	NONHSAT114586
8	lnc-MARCKS-5	chr6:114316764-114317214	NONHSAT114587

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]
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[CHB][hapmap];1.00[JPT][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[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];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[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]
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]
rs7764690	0.82[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]
rs9374432	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]
rs9481419	1.00[JPT][hapmap]
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]
rs9488315	1.00[JPT][hapmap]
rs9488316	1.00[JPT][hapmap]

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:73 , 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	chr6:114315400-114317200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:114315800-114317200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:114315800-114317200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:114315800-114317200	Enhancers	HSMM	muscle
10	chr6:114315800-114317800	Enhancers	Dnd41	blood
11	chr6:114315800-114318600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:114316000-114317200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr6:114316000-114317400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:114316000-114318400	Enhancers	Fetal Muscle Leg	muscle
15	chr6:114316200-114317000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:114316200-114317000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:114316200-114317200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr6:114316200-114317200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:114316200-114317200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:114316200-114317200	Enhancers	Brain Germinal Matrix	brain
21	chr6:114316200-114317200	Enhancers	Fetal Intestine Large	intestine
22	chr6:114316200-114317200	Enhancers	Fetal Intestine Small	intestine
23	chr6:114316200-114317200	Enhancers	Fetal Lung	lung
24	chr6:114316200-114317200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr6:114316200-114317200	Enhancers	HepG2	liver
26	chr6:114316200-114317400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:114316200-114317400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:114316200-114317600	Enhancers	Fetal Heart	heart
29	chr6:114316200-114317800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:114316200-114317800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:114316200-114317800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:114316200-114317800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:114316200-114318000	Enhancers	NH-A	brain
34	chr6:114316200-114318400	Enhancers	Adipose Nuclei	Adipose
35	chr6:114316200-114318800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:114316200-114318800	Enhancers	Rectal Smooth Muscle	rectum
37	chr6:114316200-114318800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr6:114316200-114318800	Enhancers	Stomach Smooth Muscle	stomach
39	chr6:114316200-114318800	Enhancers	HMEC	breast
40	chr6:114316200-114319000	Enhancers	NHEK	skin
41	chr6:114316200-114319200	Enhancers	NHLF	lung
42	chr6:114316200-114319200	Enhancers	Osteobl	bone
43	chr6:114316200-114320000	Enhancers	HUVEC	blood vessel
44	chr6:114316400-114317000	Flanking Active TSS	HSMMtube	muscle
45	chr6:114316400-114317000	Flanking Active TSS	NHDF-Ad	bronchial
46	chr6:114316400-114317200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr6:114316400-114317200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:114316400-114317200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:114316400-114317400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr6:114316400-114317400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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