Variant report

Variant	rs62638674
Chromosome Location	chr6:28327528-28327529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28327513-28327719	HepG2	liver:	n/a	n/a
2	TAF1	chr6:28327496-28327770	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:28327392-28327878	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:28327478-28327739	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:28327489-28327739	K562	blood:	n/a	n/a
6	POLR2A	chr6:28327459-28327678	MCF-7	breast:	n/a	n/a
7	POLR2A	chr6:28327430-28327736	MCF-7	breast:	n/a	n/a
8	POLR2A	chr6:28327523-28327786	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:28327520-28327691	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF1	chr6:28327519-28327808	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:28327445-28327708	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28327499-28327549	ECC-1	luminal epithelium:	n/a
2	chr6:28327499-28327549	GM06990	blood:	n/a
3	chr6:28327499-28327549	HRPEpiC	eye:	n/a
4	chr6:28327499-28327549	AG09319	gingival:	n/a
5	chr6:28327499-28327549	BJ	skin:	n/a
6	chr6:28327499-28327549	T-47D	breast:	n/a
7	chr6:28327499-28327549	HL-60	blood:	n/a
8	chr6:28327499-28327549	Caco-2	colon:	n/a
9	chr6:28327499-28327549	HepG2	liver:	n/a
10	chr6:28327499-28327549	PrEC	prostate:	n/a
11	chr6:28327499-28327549	Jurkat	blood:	n/a
12	chr6:28327499-28327549	ProgFib	skin:	n/a
13	chr6:28327499-28327549	H1-hESC	embryonic stem cell:	embryo
14	chr6:28327499-28327549	SKMC	muscle:	n/a
15	chr6:28327499-28327549	MCF-7	breast:	n/a
16	chr6:28327499-28327549	SK-N-SH	brain:	n/a
17	chr6:28327499-28327549	HPAEpiC	pulmonary alveolar:	n/a
18	chr6:28327499-28327549	NHBE	bronchial:	n/a
19	chr6:28327499-28327549	MCF10A-Er-Src	breast:	n/a
20	chr6:28327499-28327549	HCF	heart:	n/a
21	chr6:28327499-28327549	SAEC	small airway:	n/a
22	chr6:28327499-28327549	NH-A	brain:	n/a
23	chr6:28327499-28327549	SK-N-SH_RA	brain:	n/a
24	chr6:28327499-28327549	LNCaP	prostate:	n/a
25	chr6:28327499-28327549	BE2_C	brain:	n/a
26	chr6:28327499-28327549	HNPCEpiC	eye:	n/a
27	chr6:28327499-28327549	U87	brain:	n/a
28	chr6:28327499-28327549	HAEpiC	amniotic membrane:	n/a
29	chr6:28327499-28327549	HRCEpiC	kidney:	n/a
30	chr6:28327499-28327549	GM12878	blood:	n/a
31	chr6:28327499-28327549	NB4	blood:	n/a
32	chr6:28327499-28327549	HUVEC	blood vessel:	n/a
33	chr6:28327499-28327549	HEK293	kidney:	embryo
34	chr6:28327499-28327549	NHDF-neo	bronchial:	n/a
35	chr6:28327499-28327549	HRE	kidney:	n/a
36	chr6:28327499-28327549	Hela-S3	cervix:	n/a
37	chr6:28327499-28327549	GM12891	blood:	n/a
38	chr6:28327499-28327549	HCM	heart:	n/a
39	chr6:28327499-28327549	HCT-116	colon:	n/a
40	chr6:28327499-28327549	IMR90	lung:	fetal
41	chr6:28327499-28327549	AG09309	skin:	n/a
42	chr6:28327499-28327549	SK-N-MC	brain:	n/a
43	chr6:28327499-28327549	NT2-D1	testis:	n/a
44	chr6:28327499-28327549	GM12892	blood:	n/a
45	chr6:28327499-28327549	RPTEC	kidney:	n/a
46	chr6:28327499-28327549	HEEpiC	esophagus:	n/a
47	chr6:28327499-28327549	AG04449	skin:	fetal
48	chr6:28327499-28327549	K562	blood:	n/a
49	chr6:28327499-28327549	HCPEpiC	choroid plexus:	n/a
50	chr6:28327499-28327549	AG10803	skin:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:28326753..28329477-chr6:28335475..28338195,2	K562	blood:
2	chr6:28100726..28103259-chr6:28327481..28329415,2	K562	blood:
3	chr6:28325434..28327610-chr6:28328938..28331453,3	MCF-7	breast:
4	chr6:28323097..28326388-chr6:28326781..28330360,5	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ZSCAN31	CpG island
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1024629	1.00[AMR][1000 genomes]
rs1159276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2223287	0.83[AFR][1000 genomes]
rs28382583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28382610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35951965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36055795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56932220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57062347	1.00[AMR][1000 genomes]
rs57154605	1.00[AMR][1000 genomes]
rs57229798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57935190	0.83[AFR][1000 genomes]
rs58417073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58703563	1.00[AFR][1000 genomes]
rs58863222	1.00[AMR][1000 genomes]
rs58928655	1.00[AMR][1000 genomes]
rs59126940	1.00[AMR][1000 genomes]
rs59842349	1.00[AMR][1000 genomes]
rs60411265	0.83[AFR][1000 genomes]
rs6903306	1.00[AMR][1000 genomes]
rs6917449	1.00[AFR][1000 genomes]
rs73385824	0.83[AFR][1000 genomes]
rs73385893	1.00[AMR][1000 genomes]
rs73396315	1.00[AMR][1000 genomes]
rs73396317	1.00[AMR][1000 genomes]
rs73396335	1.00[AMR][1000 genomes]
rs73398549	0.83[AFR][1000 genomes]
rs73399102	1.00[AMR][1000 genomes]
rs73399652	1.00[AMR][1000 genomes]
rs73399679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73399695	1.00[AMR][1000 genomes]
rs73399697	1.00[AMR][1000 genomes]
rs73400304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73400305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73400511	0.83[AFR][1000 genomes]
rs73400574	0.83[AFR][1000 genomes]
rs73402526	0.83[AFR][1000 genomes]
rs73402530	0.83[AFR][1000 genomes]
rs73402963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7453044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7766194	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:28324200-28328600	Weak transcription	Primary B cells from cord blood	blood
4	chr6:28324200-28331600	Weak transcription	Thymus	Thymus
5	chr6:28324400-28327800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:28324400-28328200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:28324400-28328800	Weak transcription	Brain Anterior Caudate	brain
8	chr6:28324400-28329600	Weak transcription	Aorta	Aorta
9	chr6:28324400-28329600	Weak transcription	Fetal Intestine Small	intestine
10	chr6:28324400-28330600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:28324400-28330800	Weak transcription	Brain Substantia Nigra	brain
12	chr6:28324400-28331000	Weak transcription	Psoas Muscle	Psoas
13	chr6:28324400-28331000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:28324400-28331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:28324400-28331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:28324400-28332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:28324400-28333000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:28324400-28333000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:28324400-28333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:28324400-28336000	Weak transcription	GM12878-XiMat	blood
21	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
22	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
23	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:28324600-28328200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:28324600-28328200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:28324600-28328200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:28324600-28328200	Weak transcription	Fetal Lung	lung
30	chr6:28324600-28328200	Weak transcription	Osteobl	bone
31	chr6:28324600-28328400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:28324600-28328400	Weak transcription	HSMMtube	muscle
33	chr6:28324600-28328800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:28324600-28329200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:28324600-28329600	Weak transcription	Pancreas	Pancrea
36	chr6:28324600-28329800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:28324600-28329800	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:28324600-28330200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:28324600-28330800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:28324600-28330800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:28324600-28330800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:28324600-28330800	Weak transcription	Colonic Mucosa	Colon
43	chr6:28324600-28330800	Weak transcription	Left Ventricle	heart
44	chr6:28324600-28331000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:28324600-28331000	Weak transcription	Spleen	Spleen
46	chr6:28324600-28331200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:28324600-28331200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:28324600-28331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:28324600-28331200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:28324600-28331600	Weak transcription	Fetal Kidney	kidney

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