Variant report

Variant	rs542237866
Chromosome Location	chr6:12008961-12008962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:416)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:416 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr6:12008554-12009457	GM12878	blood:	n/a	n/a
2	GTF2F1	chr6:12008817-12008988	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZMIZ1	chr6:12008264-12009836	K562	blood:	n/a	n/a
4	STAT5A	chr6:12008337-12009358	GM12878	blood:	n/a	n/a
5	TEAD4	chr6:12008221-12009775	K562	blood:	n/a	n/a
6	TCF7L2	chr6:12008006-12009276	HEK293	kidney:	n/a	chr6:12008919-12008933
7	BHLHE40	chr6:12008368-12009828	GM12878	blood:	n/a	chr6:12009310-12009326
8	MAX	chr6:12008711-12009572	A549	lung:	n/a	chr6:12009161-12009170
9	MAX	chr6:12008484-12009867	Hela-S3	cervix:	n/a	chr6:12009161-12009170
10	MAX	chr6:12008442-12009754	A549	lung:	n/a	chr6:12009161-12009170
11	ELF1	chr6:12008504-12009412	GM12878	blood:	n/a	chr6:12009309-12009321 chr6:12009261-12009273 chr6:12009268-12009280
12	TCF12	chr6:12008658-12009386	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:12008400-12011637	K562	blood:	n/a	n/a
14	EP300	chr6:12008684-12009094	T-47D	breast:	n/a	n/a
15	FOXA1	chr6:12008721-12009024	T-47D	breast:	n/a	n/a
16	HCFC1	chr6:12008484-12009740	K562	blood:	n/a	n/a
17	POLR2A	chr6:12008545-12013822	GM18951	blood:	n/a	n/a
18	GTF2F1	chr6:12008676-12009298	K562	blood:	n/a	n/a
19	ELF1	chr6:12008560-12009076	HepG2	liver:	n/a	n/a
20	TRIM28	chr6:12008373-12009400	K562	blood:	n/a	n/a
21	E2F4	chr6:12008445-12009323	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr6:12008481-12009757	GM18526	blood:	n/a	n/a
23	POLR2A	chr6:12008516-12013922	GM19193	blood:	n/a	n/a
24	MAX	chr6:12008501-12009865	K562	blood:	n/a	chr6:12009161-12009170
25	MXI1	chr6:12008646-12009889	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:12008529-12009874	GM12878	blood:	n/a	n/a
27	GATA3	chr6:12008565-12009206	T-47D	breast:	n/a	n/a
28	POLR2A	chr6:12007817-12015834	GM12878	blood:	n/a	n/a
29	RELA	chr6:12008607-12009319	GM15510	blood:	n/a	chr6:12009245-12009254 chr6:12009245-12009254
30	POLR2A	chr6:12008475-12009815	Hela-S3	cervix:	n/a	n/a
31	RELA	chr6:12008424-12009289	GM18505	blood:	n/a	chr6:12009245-12009254 chr6:12009245-12009254
32	ETS1	chr6:12008639-12009382	GM12878	blood:	n/a	n/a
33	TAF1	chr6:12008483-12009072	GM12891	blood:	n/a	n/a
34	TAF1	chr6:12008489-12009814	GM12878	blood:	n/a	n/a
35	CCNT2	chr6:12008406-12009802	K562	blood:	n/a	n/a
36	POLR2A	chr6:12008727-12009407	PANC-1	pancreas:	n/a	n/a
37	ZBTB7A	chr6:12008725-12009098	HepG2	liver:	n/a	n/a
38	POLR2A	chr6:12008496-12009441	HCT-116	colon:	n/a	n/a
39	POLR2A	chr6:12008458-12009369	SK-N-SH	brain:	n/a	n/a
40	FOXM1	chr6:12008506-12009378	GM12878	blood:	n/a	n/a
41	RFX5	chr6:12008605-12009284	HepG2	liver:	n/a	n/a
42	EP300	chr6:12008587-12009316	HepG2	liver:	n/a	chr6:12009255-12009271
43	TCF12	chr6:12008535-12009612	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr6:12007783-12012797	K562	blood:	n/a	n/a
45	EGR1	chr6:12008713-12009583	GM12878	blood:	n/a	n/a
46	IKZF1	chr6:12008591-12009160	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:12008635-12009324	U87	brain:	n/a	n/a
48	GATA2	chr6:12008487-12009140	K562	blood:	n/a	n/a
49	TEAD4	chr6:12008773-12009785	SK-N-SH	brain:	n/a	n/a
50	RAD21	chr6:12008542-12009052	SK-N-SH_RA	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:4475034..4475714-chr6:12008711..12009473,2	Hela-S3	cervix:
2	chr6:11990947..11994181-chr6:12007149..12010077,3	K562	blood:
3	chr6:11804488..11807450-chr6:12008603..12011488,3	MCF-7	breast:
4	chr6:11766846..11771135-chr6:12008831..12011747,3	K562	blood:
5	chr6:12008844..12009838-chr7:134854735..134855590,2	Hela-S3	cervix:
6	chr19:15442596..15443457-chr6:12008582..12009195,2	Hela-S3	cervix:
7	chr12:57029606..57030383-chr6:12008234..12009003,2	Hela-S3	cervix:
8	chr1:109968661..109969227-chr6:12008493..12009023,2	Hela-S3	cervix:
9	chr11:66383680..66384551-chr6:12008610..12009525,2	Hela-S3	cervix:
10	chr6:12008600..12009379-chr6:43737966..43738894,2	Hela-S3	cervix:
11	chr15:78556049..78556549-chr6:12008716..12009219,2	Hela-S3	cervix:
12	chr6:11733150..11736062-chr6:12007778..12010289,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIVEP1-1	chr6:12008512-12009089	ENSG00000229896.1
2	lnc-C6orf105-5	chr6:12008548-12009073	NONHSAT107775

No data

Variant related genes	Relation type
HIVEP1	TF binding region
ENSG00000141867	Chromatin interaction
ENSG00000225102	Chromatin interaction
ENSG00000140403	Chromatin interaction
ENSG00000143106	Chromatin interaction
ENSG00000272114	Chromatin interaction
ENSG00000111863	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000112715	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000262246	Chromatin interaction
ENSG00000122783	Chromatin interaction
ENSG00000259708	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	nsv970323	chr6:12006884-12020375	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv10446	chr6:12008060-12013799	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12007400-12013400	Active TSS	K562	blood
2	chr6:12007800-12009800	Active TSS	Liver	Liver
3	chr6:12007800-12009800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:12007800-12009800	Bivalent/Poised TSS	HepG2	liver
5	chr6:12007800-12011400	Active TSS	Fetal Muscle Trunk	muscle
6	chr6:12008000-12009000	Active TSS	Fetal Brain Male	brain
7	chr6:12008000-12014000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:12008200-12009000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:12008200-12009200	Flanking Active TSS	HMEC	breast
10	chr6:12008200-12009800	Active TSS	Fetal Intestine Large	intestine
11	chr6:12008200-12010200	Active TSS	A549	lung
12	chr6:12008200-12010600	Active TSS	Fetal Muscle Leg	muscle
13	chr6:12008200-12014000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:12008400-12009000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr6:12008400-12009000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr6:12008400-12009000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:12008400-12009000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr6:12008400-12009000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr6:12008400-12009000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:12008400-12009000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr6:12008400-12009000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:12008400-12009000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr6:12008400-12009000	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr6:12008400-12009000	Flanking Active TSS	Fetal Thymus	thymus
25	chr6:12008400-12009000	Flanking Active TSS	Dnd41	blood
26	chr6:12008400-12009000	Flanking Active TSS	HUVEC	blood vessel
27	chr6:12008400-12009600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:12008400-12009600	Active TSS	Brain Cingulate Gyrus	brain
29	chr6:12008400-12009600	Active TSS	Left Ventricle	heart
30	chr6:12008400-12009800	Active TSS	Pancreas	Pancrea
31	chr6:12008400-12010000	Active TSS	Brain Anterior Caudate	brain
32	chr6:12008400-12010000	Active TSS	Stomach Smooth Muscle	stomach
33	chr6:12008400-12010000	Active TSS	HSMMtube	muscle
34	chr6:12008400-12010800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:12008400-12010800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:12008400-12011400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr6:12008400-12011600	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr6:12008400-12013600	Active TSS	Psoas Muscle	Psoas
39	chr6:12008400-12013800	Active TSS	Right Ventricle	heart
40	chr6:12008400-12014200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:12008600-12009000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr6:12008600-12009000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:12008600-12009000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:12008600-12009000	Flanking Active TSS	HSMM	muscle
45	chr6:12008600-12009200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:12008600-12009600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:12008600-12009600	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr6:12008600-12009600	Active TSS	Fetal Heart	heart
49	chr6:12008600-12009800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:12008600-12009800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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