Variant report

Variant	rs6906990
Chromosome Location	chr6:166879653-166879654
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	TCF12	chr6:166879437-166880231	ECC-1	luminal epithelium:	n/a	chr6:166879856-166879864
2	CEBPB	chr6:166879642-166879983	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr6:166879600-166879750	WI-38	lung:	n/a	n/a
4	CTCF	chr6:166879580-166879730	AoAF	blood vessel:	n/a	n/a
5	CTCF	chr6:166879640-166879790	SK-N-SH_RA	brain:	n/a	n/a
6	NFIC	chr6:166879550-166880207	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr6:166879418-166880295	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr6:166879620-166879770	HPAF	blood vessel:	n/a	n/a
9	CTCF	chr6:166879520-166879670	HRPEpiC	eye:	n/a	n/a
10	MAX	chr6:166879573-166880204	ECC-1	luminal epithelium:	n/a	n/a
11	PBX3	chr6:166879489-166880442	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr6:166879580-166879730	HPF	lung:	n/a	n/a
13	SIN3AK20	chr6:166879602-166880065	SK-N-SH	brain:	n/a	n/a
14	REST	chr6:166879648-166880002	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr6:166879600-166879750	AoAF	blood vessel:	n/a	n/a
16	EP300	chr6:166879588-166880143	ECC-1	luminal epithelium:	n/a	chr6:166879679-166879689 chr6:166879820-166879827
17	CTCF	chr6:166879620-166879770	HAc	cerebellar:	n/a	n/a
18	CTCF	chr6:166879640-166879790	HEK293	kidney:	n/a	n/a
19	CTCF	chr6:166879620-166879770	AG04449	skin:	n/a	n/a
20	TCF12	chr6:166879546-166880357	ECC-1	luminal epithelium:	n/a	chr6:166879856-166879864
21	POLR2A	chr6:166878145-166882263	PFSK-1	brain:	n/a	n/a
22	FOSL2	chr6:166879542-166880561	SK-N-SH	brain:	n/a	chr6:166879957-166879967 chr6:166880169-166880180
23	TEAD4	chr6:166879472-166880270	ECC-1	luminal epithelium:	n/a	n/a
24	CTCF	chr6:166879600-166879750	HPAF	blood vessel:	n/a	n/a
25	CTCF	chr6:166879600-166879750	HepG2	liver:	n/a	n/a
26	TCF12	chr6:166879221-166880478	SK-N-SH	brain:	n/a	chr6:166879272-166879282 chr6:166879856-166879864
27	TAF1	chr6:166879602-166879948	SK-N-SH	brain:	n/a	n/a
28	RAD21	chr6:166879262-166879936	IMR90	lung:	n/a	n/a
29	POLR2A	chr6:166879583-166880059	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr6:166879243-166880393	SK-N-SH	brain:	n/a	chr6:166879272-166879282 chr6:166879856-166879864
31	TAF1	chr6:166879595-166881068	PFSK-1	brain:	n/a	n/a
32	CTCF	chr6:166879640-166879790	BJ	skin:	n/a	n/a
33	EP300	chr6:166879461-166880267	ECC-1	luminal epithelium:	n/a	chr6:166879679-166879689 chr6:166879820-166879827
34	MAX	chr6:166879587-166880189	SK-N-SH	brain:	n/a	n/a
35	PBX3	chr6:166879257-166880491	SK-N-SH	brain:	n/a	chr6:166879413-166879422
36	CTCF	chr6:166879560-166879710	HPF	lung:	n/a	n/a
37	TEAD4	chr6:166879494-166880181	ECC-1	luminal epithelium:	n/a	n/a
38	CTCF	chr6:166879580-166879730	AG10803	skin:	n/a	n/a
39	JUND	chr6:166879443-166880476	SK-N-SH	brain:	n/a	chr6:166880225-166880236 chr6:166880257-166880268 chr6:166879957-166879967 chr6:166880205-166880216 chr6:166880169-166880180
40	CTCF	chr6:166879127-166879689	A549	lung:	n/a	n/a
41	POLR2A	chr6:166879577-166880157	ECC-1	luminal epithelium:	n/a	n/a
42	TEAD4	chr6:166879363-166880181	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr6:166878957-166882136	PFSK-1	brain:	n/a	n/a
44	CTCF	chr6:166879640-166879790	HBMEC	blood vessel:	n/a	n/a
45	POLR2A	chr6:166879631-166879746	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166871889..166873613-chr6:166879410..166881105,2	K562	blood:

Variant related genes	Relation type
RPS6KA2-IT1	TF binding region
ENSG00000071242	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16899079	1.00[CEU][hapmap]
rs16899149	1.00[CEU][hapmap]
rs4473841	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886937	chr6:166830696-166922813	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886938	chr6:166859725-166904398	Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv886939	chr6:166859725-166922813	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166808200-166911800	Weak transcription	Psoas Muscle	Psoas
2	chr6:166824000-166901400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:166846000-166881000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:166862400-166900600	Weak transcription	Primary T cells from cord blood	blood
5	chr6:166862400-166920600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:166862600-166883000	Weak transcription	Aorta	Aorta
7	chr6:166862600-166883000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:166863600-166900200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:166863600-166902000	Weak transcription	Small Intestine	intestine
10	chr6:166864600-166883000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:166864800-166899800	Weak transcription	Esophagus	oesophagus
12	chr6:166867400-166892800	Weak transcription	Fetal Brain Male	brain
13	chr6:166867600-166900000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:166870400-166898400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:166870600-166881000	Weak transcription	Fetal Kidney	kidney
16	chr6:166871000-166901400	Weak transcription	Stomach Mucosa	stomach
17	chr6:166872000-166900400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:166872200-166900400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:166873000-166902800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:166874200-166885200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:166874800-166880600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:166874800-166903000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:166875000-166881000	Weak transcription	NHEK	skin
24	chr6:166875000-166900800	Weak transcription	Fetal Heart	heart
25	chr6:166875400-166881200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:166875400-166885400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:166875600-166884200	Strong transcription	Gastric	stomach
28	chr6:166875800-166883000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:166875800-166883200	Weak transcription	HMEC	breast
30	chr6:166875800-166887000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:166875800-166894000	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:166876000-166881200	Strong transcription	Fetal Brain Female	brain
33	chr6:166876000-166883800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:166876000-166885000	Strong transcription	Right Ventricle	heart
35	chr6:166876000-166888800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:166876000-166901400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:166876200-166886600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:166876600-166880000	Strong transcription	Lung	lung
39	chr6:166877000-166885200	Strong transcription	Spleen	Spleen
40	chr6:166877200-166880200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:166877200-166880400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:166877200-166904400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:166877200-166908800	Weak transcription	Colonic Mucosa	Colon
44	chr6:166877400-166883800	Strong transcription	Brain Germinal Matrix	brain
45	chr6:166877600-166885200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:166877800-166881800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr6:166878000-166880200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:166878000-166880600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:166878200-166880200	Enhancers	Fetal Muscle Leg	muscle
50	chr6:166878200-166902000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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