Variant report

Variant	rs628572
Chromosome Location	chr6:16765502-16765503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr6:16765444-16765793	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:16765403-16765563	MCF10A-Er-Src	breast:	n/a	n/a
3	SMC3	chr6:16764384-16765774	SK-N-SH	brain:	n/a	chr6:16765002-16765016
4	RAD21	chr6:16764421-16765737	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:16765484-16765534	T-47D	breast:	n/a
2	chr6:16765484-16765534	GM19239	blood:	n/a
3	chr6:16765484-16765534	AG04449	skin:	fetal
4	chr6:16765484-16765534	HCF	heart:	n/a
5	chr6:16765484-16765534	NB4	blood:	n/a
6	chr6:16765484-16765534	HNPCEpiC	eye:	n/a
7	chr6:16765484-16765534	CMK	blood:	n/a
8	chr6:16765484-16765534	HIPEpiC	eye:	n/a
9	chr6:16765484-16765534	GM12878	blood:	n/a
10	chr6:16765484-16765534	H1-hESC	embryonic stem cell:	embryo
11	chr6:16765484-16765534	HUVEC	blood vessel:	n/a
12	chr6:16765484-16765534	AG09319	gingival:	n/a
13	chr6:16765484-16765534	HEK293	kidney:	embryo
14	chr6:16765484-16765534	HRE	kidney:	n/a
15	chr6:16765484-16765534	RPTEC	kidney:	n/a
16	chr6:16765484-16765534	SK-N-MC	brain:	n/a
17	chr6:16765484-16765534	NH-A	brain:	n/a
18	chr6:16765484-16765534	AG10803	skin:	n/a
19	chr6:16765484-16765534	HCPEpiC	choroid plexus:	n/a
20	chr6:16765484-16765534	ECC-1	luminal epithelium:	n/a
21	chr6:16765484-16765534	Hepatocyte	liver:	n/a
22	chr6:16765484-16765534	MCF10A-Er-Src	breast:	n/a
23	chr6:16765484-16765534	BJ	skin:	n/a
24	chr6:16765484-16765534	Hela-S3	cervix:	n/a
25	chr6:16765484-16765534	MCF-7	breast:	n/a
26	chr6:16765484-16765534	Jurkat	blood:	n/a
27	chr6:16765484-16765534	A549	lung:	n/a
28	chr6:16765484-16765534	AG04450	lung:	fetal
29	chr6:16765484-16765534	HEEpiC	esophagus:	n/a
30	chr6:16765484-16765534	HepG2	liver:	n/a
31	chr6:16765484-16765534	HAEpiC	amniotic membrane:	n/a
32	chr6:16765484-16765534	HPAEpiC	pulmonary alveolar:	n/a
33	chr6:16765484-16765534	HRPEpiC	eye:	n/a
34	chr6:16765484-16765534	GM12892	blood:	n/a
35	chr6:16765484-16765534	PANC-1	pancreas:	n/a
36	chr6:16765484-16765534	NHBE	bronchial:	n/a
37	chr6:16765484-16765534	LNCaP	prostate:	n/a
38	chr6:16765484-16765534	GM12891	blood:	n/a
39	chr6:16765484-16765534	HRCEpiC	kidney:	n/a
40	chr6:16765484-16765534	ovcar-3	ovarian:	n/a
41	chr6:16765484-16765534	IMR90	lung:	fetal
42	chr6:16765484-16765534	BE2_C	brain:	n/a
43	chr6:16765484-16765534	SK-N-SH_RA	brain:	n/a
44	chr6:16765484-16765534	GM06990	blood:	n/a
45	chr6:16765484-16765534	NT2-D1	testis:	n/a
46	chr6:16765484-16765534	PFSK-1	brain:	n/a
47	chr6:16765484-16765534	SK-N-SH	brain:	n/a
48	chr6:16765484-16765534	HCT-116	colon:	n/a
49	chr6:16765484-16765534	AG09309	skin:	n/a
50	chr6:16765484-16765534	ProgFib	skin:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:16683098..16685011-chr6:16765280..16767856,2	MCF-7	breast:
2	chr6:16765001..16766540-chr6:17090173..17092560,2	MCF-7	breast:
3	chr6:16764746..16767441-chr6:16826429..16828580,2	MCF-7	breast:
4	chr6:16765000..16765622-chr6:17093681..17094432,2	MCF-7	breast:
5	chr6:16764759..16765583-chr6:16820122..16820707,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP3-486B10.1.1-1	chr6:16761828-16766981	NONHSAT107909
2	lnc-RP3-486B10.1.1-1	chr6:16764577-16767114	ENSG00000272341.1

No data

Variant related genes	Relation type
ATXN1	TF binding region
ATXN1	CpG island

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12664358	0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16762800-16765600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr6:16763000-16769400	Weak transcription	Lung	lung
3	chr6:16763000-16769400	Weak transcription	Small Intestine	intestine
4	chr6:16763200-16766400	Weak transcription	K562	blood
5	chr6:16763200-16767200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:16763200-16769400	Weak transcription	Pancreas	Pancrea
7	chr6:16763200-16769600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:16763200-16770800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:16763400-16765600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr6:16763400-16765600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:16763400-16766400	Weak transcription	Stomach Mucosa	stomach
12	chr6:16763400-16767200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:16763400-16768600	Weak transcription	Primary T cells from cord blood	blood
14	chr6:16763400-16768800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:16763400-16768800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:16763400-16771200	Weak transcription	Placenta	Placenta
17	chr6:16763600-16765800	Enhancers	Rectal Smooth Muscle	rectum
18	chr6:16763600-16766400	Weak transcription	Fetal Lung	lung
19	chr6:16763600-16768000	Weak transcription	Adipose Nuclei	Adipose
20	chr6:16763600-16768600	Weak transcription	Fetal Kidney	kidney
21	chr6:16763600-16769000	Weak transcription	Brain Substantia Nigra	brain
22	chr6:16763800-16765600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:16763800-16765600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:16763800-16765800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:16763800-16766000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:16763800-16766000	Enhancers	A549	lung
27	chr6:16763800-16766400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:16763800-16766400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:16763800-16766400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:16763800-16766600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:16763800-16766800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:16763800-16767200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:16763800-16767200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:16763800-16767400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:16763800-16767800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:16763800-16768200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:16763800-16768200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:16763800-16768400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:16763800-16768600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:16763800-16768600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr6:16763800-16768800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:16763800-16768800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:16763800-16768800	Weak transcription	Fetal Brain Male	brain
44	chr6:16763800-16768800	Weak transcription	Left Ventricle	heart
45	chr6:16763800-16768800	Weak transcription	Right Ventricle	heart
46	chr6:16763800-16769000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:16763800-16769200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:16763800-16770800	Weak transcription	Fetal Intestine Small	intestine
49	chr6:16763800-16771200	Weak transcription	Brain Hippocampus Middle	brain
50	chr6:16764000-16765600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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