Variant report

Variant	rs2097424
Chromosome Location	chr6:28878214-28878215
allele	C/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:1)
LncRNA
region (count:0)
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	POLR2A	chr6:28877033-28879022	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr6:28877136-28879784	K562	blood:	n/a	n/a
3	POLR2A	chr6:28877163-28879808	K562	blood:	n/a	n/a
4	POLR2A	chr6:28876413-28878953	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28878192-28878242	ovcar-3	ovarian:	n/a
2	chr6:28878192-28878242	AG10803	skin:	n/a
3	chr6:28878192-28878242	HPAEpiC	pulmonary alveolar:	n/a
4	chr6:28878192-28878242	SK-N-MC	brain:	n/a
5	chr6:28878192-28878242	HCPEpiC	choroid plexus:	n/a
6	chr6:28878192-28878242	HAEpiC	amniotic membrane:	n/a
7	chr6:28878192-28878242	SK-N-SH	brain:	n/a
8	chr6:28878192-28878242	BE2_C	brain:	n/a
9	chr6:28878192-28878242	AG04450	lung:	fetal
10	chr6:28878192-28878242	PFSK-1	brain:	n/a
11	chr6:28878192-28878242	AG09319	gingival:	n/a
12	chr6:28878192-28878242	GM06990	blood:	n/a
13	chr6:28878192-28878242	NT2-D1	testis:	n/a
14	chr6:28878192-28878242	NB4	blood:	n/a
15	chr6:28878192-28878242	RPTEC	kidney:	n/a
16	chr6:28878192-28878242	HRE	kidney:	n/a
17	chr6:28878192-28878242	ProgFib	skin:	n/a
18	chr6:28878192-28878242	K562	blood:	n/a
19	chr6:28878192-28878242	HRCEpiC	kidney:	n/a
20	chr6:28878192-28878242	SKMC	muscle:	n/a
21	chr6:28878192-28878242	U87	brain:	n/a
22	chr6:28878192-28878242	LNCaP	prostate:	n/a
23	chr6:28878192-28878242	HepG2	liver:	n/a
24	chr6:28878192-28878242	SK-N-SH_RA	brain:	n/a
25	chr6:28878192-28878242	HL-60	blood:	n/a
26	chr6:28878192-28878242	NH-A	brain:	n/a
27	chr6:28878192-28878242	IMR90	lung:	fetal
28	chr6:28878192-28878242	BJ	skin:	n/a
29	chr6:28878192-28878242	GM19239	blood:	n/a
30	chr6:28878192-28878242	PANC-1	pancreas:	n/a
31	chr6:28878192-28878242	AG04449	skin:	fetal
32	chr6:28878192-28878242	HNPCEpiC	eye:	n/a
33	chr6:28878192-28878242	Hepatocyte	liver:	n/a
34	chr6:28878192-28878242	HIPEpiC	eye:	n/a
35	chr6:28878192-28878242	MCF-7	breast:	n/a
36	chr6:28878192-28878242	NHBE	bronchial:	n/a
37	chr6:28878192-28878242	HCT-116	colon:	n/a
38	chr6:28878192-28878242	PrEC	prostate:	n/a
39	chr6:28878192-28878242	ECC-1	luminal epithelium:	n/a
40	chr6:28878192-28878242	HCM	heart:	n/a
41	chr6:28878192-28878242	HMEC	breast:	n/a
42	chr6:28878192-28878242	HEK293	kidney:	embryo
43	chr6:28878192-28878242	HEEpiC	esophagus:	n/a
44	chr6:28878192-28878242	GM12878	blood:	n/a
45	chr6:28878192-28878242	Jurkat	blood:	n/a
46	chr6:28878192-28878242	GM12891	blood:	n/a
47	chr6:28878192-28878242	NHDF-neo	bronchial:	n/a
48	chr6:28878192-28878242	HRPEpiC	eye:	n/a
49	chr6:28878192-28878242	AoSMC	blood vessel:	n/a
50	chr6:28878192-28878242	Caco-2	colon:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28874958..28881784-chr6:28883001..28892669,21	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM27	TF binding region
TRIM27	CpG island
ENSG00000204713	Chromatin interaction
ENSG00000212240	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1061625	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs172326	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1794588	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184094	0.83[ASN][1000 genomes]
rs2013652	0.81[EUR][1000 genomes]
rs209127	0.92[ASN][1000 genomes]
rs209140	0.88[ASN][1000 genomes]
rs209147	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209151	0.86[ASN][1000 genomes]
rs209165	0.87[ASN][1000 genomes]
rs209172	0.86[ASN][1000 genomes]
rs209177	0.85[ASN][1000 genomes]
rs209180	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2148007	0.81[ASN][1000 genomes]
rs2269553	0.86[ASN][1000 genomes]
rs2894066	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130843	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3131067	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131098	0.82[ASN][1000 genomes]
rs3132377	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3132380	0.89[ASN][1000 genomes]
rs3135314	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs393309	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs413972	0.88[ASN][1000 genomes]
rs422331	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs429369	0.87[ASN][1000 genomes]
rs4484511	0.81[ASN][1000 genomes]
rs6906953	0.85[ASN][1000 genomes]
rs6912843	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6926892	0.81[ASN][1000 genomes]
rs7750338	0.87[ASN][1000 genomes]
rs7769221	0.87[ASN][1000 genomes]
rs876737	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9257328	0.87[ASN][1000 genomes]
rs9257395	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9257399	0.81[ASN][1000 genomes]
rs9257416	0.82[ASN][1000 genomes]
rs9257425	0.81[ASN][1000 genomes]
rs929042	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28866000-28887000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28867000-28889400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:28867600-28889200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28867600-28889400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:28867600-28889600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:28867800-28878800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:28867800-28880000	Strong transcription	Primary T cells from cord blood	blood
8	chr6:28867800-28881600	Strong transcription	HSMM	muscle
9	chr6:28867800-28883200	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr6:28867800-28885400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:28867800-28888200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:28867800-28888400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:28867800-28888400	Strong transcription	Fetal Thymus	thymus
14	chr6:28867800-28889200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:28867800-28889200	Strong transcription	HMEC	breast
16	chr6:28867800-28889400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:28867800-28889400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:28867800-28889600	Strong transcription	Fetal Lung	lung
19	chr6:28868000-28878400	Strong transcription	Placenta	Placenta
20	chr6:28868000-28889200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:28868200-28880200	Strong transcription	Primary hematopoietic stem cells	blood
22	chr6:28868200-28887200	Strong transcription	HUVEC	blood vessel
23	chr6:28868200-28889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:28868200-28889800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:28868400-28878400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:28868400-28878400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:28868400-28878600	Strong transcription	NHEK	skin
28	chr6:28868400-28879600	Strong transcription	Brain Cingulate Gyrus	brain
29	chr6:28868400-28879800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:28868400-28879800	Strong transcription	GM12878-XiMat	blood
31	chr6:28868400-28880200	Strong transcription	Thymus	Thymus
32	chr6:28868400-28880600	Strong transcription	Brain Germinal Matrix	brain
33	chr6:28868400-28881000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:28868400-28881000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:28868400-28881600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr6:28868400-28882600	Strong transcription	Liver	Liver
37	chr6:28868400-28884400	Strong transcription	Dnd41	blood
38	chr6:28868400-28886800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:28868400-28887200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:28868400-28888400	Strong transcription	Adipose Nuclei	Adipose
41	chr6:28868400-28888400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr6:28868400-28888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:28868400-28888400	Strong transcription	Fetal Brain Female	brain
44	chr6:28868400-28888400	Strong transcription	Fetal Muscle Leg	muscle
45	chr6:28868400-28888600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:28868400-28889000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:28868400-28889200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr6:28868400-28889400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr6:28868400-28889400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:28868600-28878400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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