Variant report

Variant	rs209140
Chromosome Location	chr6:28863469-28863470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:340)
CpG islands
(count:61)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:340 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr6:28863121-28863557	GM12878	blood:	n/a	n/a
2	RCOR1	chr6:28863220-28863652	GM12878	blood:	n/a	n/a
3	MYC	chr6:28863154-28863568	NB4	blood:	n/a	n/a
4	ZBTB33	chr6:28863089-28863768	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:28863088-28863649	HL-60	blood:	n/a	n/a
6	MBD4	chr6:28862979-28863543	HepG2	liver:	n/a	n/a
7	TEAD4	chr6:28863046-28864424	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:28863143-28865216	K562	blood:	n/a	n/a
9	ZBTB33	chr6:28863195-28863752	K562	blood:	n/a	n/a
10	HEY1	chr6:28862979-28863779	K562	blood:	n/a	n/a
11	IRF1	chr6:28863021-28864300	K562	blood:	n/a	n/a
12	TAF1	chr6:28863234-28863618	MCF-7	breast:	n/a	n/a
13	POLR2A	chr6:28863013-28863774	K562	blood:	n/a	n/a
14	HMGN3	chr6:28863202-28863532	K562	blood:	n/a	n/a
15	POLR2A	chr6:28863126-28863774	H1-hESC	embryonic stem cell:	n/a	n/a
16	POU2F2	chr6:28863033-28863615	GM12891	blood:	n/a	chr6:28863144-28863166
17	ELF1	chr6:28863114-28863597	MCF-7	breast:	n/a	n/a
18	YY1	chr6:28863205-28863594	ECC-1	luminal epithelium:	n/a	n/a
19	TAF1	chr6:28863177-28863537	GM12892	blood:	n/a	n/a
20	POLR2A	chr6:28863051-28863711	SK-N-MC	brain:	n/a	n/a
21	YY1	chr6:28863197-28863569	HCT-116	colon:	n/a	n/a
22	POLR2A	chr6:28863018-28863714	GM12892	blood:	n/a	n/a
23	TEAD4	chr6:28862971-28865457	K562	blood:	n/a	n/a
24	POLR2A	chr6:28862972-28865222	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr6:28863177-28863560	SK-N-SH	brain:	n/a	n/a
26	SETDB1	chr6:28863079-28863607	U2OS	brain:	n/a	n/a
27	STAT3	chr6:28863238-28863546	MCF10A-Er-Src	breast:	n/a	chr6:28863397-28863405
28	JUND	chr6:28863174-28863608	K562	blood:	n/a	n/a
29	RUNX3	chr6:28863207-28863657	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:28863273-28863480	A549	lung:	n/a	n/a
31	GATA1	chr6:28863056-28863717	PBDE	blood:	n/a	n/a
32	POLR2A	chr6:28863176-28863575	A549	lung:	n/a	n/a
33	POLR2A	chr6:28863124-28865156	HepG2	liver:	n/a	n/a
34	POU2F2	chr6:28863125-28863577	GM12891	blood:	n/a	chr6:28863144-28863166
35	ETS1	chr6:28863218-28863707	GM12878	blood:	n/a	chr6:28863527-28863536 chr6:28863508-28863517 chr6:28863289-28863302 chr6:28863530-28863539
36	POLR2A	chr6:28863109-28864339	MCF-7	breast:	n/a	n/a
37	ZNF384	chr6:28863218-28865143	K562	blood:	n/a	n/a
38	ZBTB33	chr6:28863001-28863711	HepG2	liver:	n/a	n/a
39	GTF2B	chr6:28863185-28863596	K562	blood:	n/a	n/a
40	BRCA1	chr6:28863036-28864465	Hela-S3	cervix:	n/a	n/a
41	E2F6	chr6:28863016-28863674	A549	lung:	n/a	chr6:28863350-28863357 chr6:28863347-28863358 chr6:28863350-28863357 chr6:28863350-28863357
42	ZBTB33	chr6:28863075-28863717	GM12878	blood:	n/a	n/a
43	SIN3AK20	chr6:28863167-28863691	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr6:28863021-28863631	K562	blood:	n/a	n/a
45	TAF1	chr6:28863190-28863597	SK-N-SH	brain:	n/a	n/a
46	REST	chr6:28863205-28863502	K562	blood:	n/a	n/a
47	POLR2A	chr6:28863028-28864493	PFSK-1	brain:	n/a	n/a
48	MAX	chr6:28863077-28863669	ECC-1	luminal epithelium:	n/a	n/a
49	GTF2F1	chr6:28863173-28863646	Hela-S3	cervix:	n/a	n/a
50	GATA3	chr6:28863044-28863637	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	chr6:28863428-28863478	H1-hESC	embryonic stem cell:	embryo
2	chr6:28863428-28863478	NHDF-neo	bronchial:	n/a
3	chr6:28863428-28863478	AoSMC	blood vessel:	n/a
4	chr6:28863428-28863478	PANC-1	pancreas:	n/a
5	chr6:28863428-28863478	SKMC	muscle:	n/a
6	chr6:28863428-28863478	HCM	heart:	n/a
7	chr6:28863428-28863478	HUVEC	blood vessel:	n/a
8	chr6:28863428-28863478	BJ	skin:	n/a
9	chr6:28863428-28863478	MCF10A-Er-Src	breast:	n/a
10	chr6:28863428-28863478	Caco-2	colon:	n/a
11	chr6:28863428-28863478	Hepatocyte	liver:	n/a
12	chr6:28863428-28863478	GM12892	blood:	n/a
13	chr6:28863428-28863478	HRCEpiC	kidney:	n/a
14	chr6:28863428-28863478	ProgFib	skin:	n/a
15	chr6:28863428-28863478	PFSK-1	brain:	n/a
16	chr6:28863428-28863478	SK-N-SH	brain:	n/a
17	chr6:28863428-28863478	HAEpiC	amniotic membrane:	n/a
18	chr6:28863428-28863478	ECC-1	luminal epithelium:	n/a
19	chr6:28863428-28863478	SK-N-SH_RA	brain:	n/a
20	chr6:28863428-28863478	CMK	blood:	n/a
21	chr6:28863428-28863478	HEK293	kidney:	embryo
22	chr6:28863428-28863478	HIPEpiC	eye:	n/a
23	chr6:28863428-28863478	Jurkat	blood:	n/a
24	chr6:28863428-28863478	GM12878	blood:	n/a
25	chr6:28863428-28863478	HCPEpiC	choroid plexus:	n/a
26	chr6:28863428-28863478	HRPEpiC	eye:	n/a
27	chr6:28863428-28863478	BE2_C	brain:	n/a
28	chr6:28863428-28863478	A549	lung:	n/a
29	chr6:28863428-28863478	SK-N-MC	brain:	n/a
30	chr6:28863428-28863478	AG04449	skin:	fetal
31	chr6:28863428-28863478	MCF-7	breast:	n/a
32	chr6:28863428-28863478	ovcar-3	ovarian:	n/a
33	chr6:28863428-28863478	NH-A	brain:	n/a
34	chr6:28863428-28863478	IMR90	lung:	fetal
35	chr6:28863428-28863478	AG09319	gingival:	n/a
36	chr6:28863428-28863478	HL-60	blood:	n/a
37	chr6:28863428-28863478	HNPCEpiC	eye:	n/a
38	chr6:28863428-28863478	NHBE	bronchial:	n/a
39	chr6:28863428-28863478	AG09309	skin:	n/a
40	chr6:28863428-28863478	NT2-D1	testis:	n/a
41	chr6:28863428-28863478	T-47D	breast:	n/a
42	chr6:28863428-28863478	AG10803	skin:	n/a
43	chr6:28863428-28863478	AG04450	lung:	fetal
44	chr6:28863428-28863478	HCF	heart:	n/a
45	chr6:28863428-28863478	Hela-S3	cervix:	n/a
46	chr6:28863428-28863478	GM06990	blood:	n/a
47	chr6:28863428-28863478	HPAEpiC	pulmonary alveolar:	n/a
48	chr6:28863428-28863478	HEEpiC	esophagus:	n/a
49	chr6:28863428-28863478	SAEC	small airway:	n/a
50	chr6:28863428-28863478	LNCaP	prostate:	n/a

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28761882..28764605-chr6:28861705..28864953,3	K562	blood:
2	chr6:28861105..28864204-chr6:28976259..28979273,3	K562	blood:
3	chr12:52541567..52542139-chr6:28863024..28863573,2	Hela-S3	cervix:
4	chr6:28830882..28836292-chr6:28860588..28866545,10	MCF-7	breast:
5	chr16:2014065..2015046-chr6:28863401..28864148,2	Hela-S3	cervix:
6	chr6:28803400..28808440-chr6:28861740..28869149,12	K562	blood:
7	chr6:28828478..28839935-chr6:28855092..28866386,31	K562	blood:
8	chr6:28861427..28866893-chr6:28947878..28954176,14	K562	blood:
9	chr6:28675753..28677785-chr6:28861605..28864200,2	K562	blood:
10	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
11	chr6:28823280..28824942-chr6:28861506..28864174,2	K562	blood:
12	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
13	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
14	chr6:28823126..28835109-chr6:28859268..28867076,23	K562	blood:
15	chr17:80231345..80232026-chr6:28862952..28863692,2	HCT-116	colon:
16	chr6:28862538..28864081-chr6:28971879..28974457,2	K562	blood:
17	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:
18	chr6:28802724..28808694-chr6:28856997..28865691,21	K562	blood:
19	chr6:28858686..28861504-chr6:28861818..28863578,3	MCF-7	breast:
20	chr6:28853385..28858171-chr6:28860346..28864278,7	MCF-7	breast:

No data

Variant related genes	Relation type
HCG14	TF binding region
HCG14	CpG island
ENSG00000255513	Chromatin interaction
ENSG00000141551	Chromatin interaction
ENSG00000213916	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000265764	Chromatin interaction
ENSG00000140988	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1061625	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs172326	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1794588	0.89[ASN][1000 genomes]
rs184094	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2013652	0.83[ASN][1000 genomes]
rs209127	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209147	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs209151	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs209165	0.93[ASN][1000 genomes]
rs209172	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209177	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209180	0.88[ASN][1000 genomes]
rs2097424	0.88[ASN][1000 genomes]
rs2148007	0.90[ASN][1000 genomes]
rs2269553	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28381661	0.81[ASN][1000 genomes]
rs28381663	0.80[ASN][1000 genomes]
rs28743260	0.81[ASN][1000 genomes]
rs2894066	0.90[ASN][1000 genomes]
rs3130843	0.81[ASN][1000 genomes]
rs3131067	0.83[ASN][1000 genomes]
rs3132377	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3132380	0.86[ASN][1000 genomes]
rs3135314	0.90[ASN][1000 genomes]
rs393309	0.81[ASN][1000 genomes]
rs413972	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs422331	0.91[ASN][1000 genomes]
rs429369	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4484511	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6909419	0.80[ASN][1000 genomes]
rs6912843	0.84[ASN][1000 genomes]
rs743847	0.88[ASN][1000 genomes]
rs7750338	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7763940	0.81[ASN][1000 genomes]
rs7769221	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776376	0.81[ASN][1000 genomes]
rs876737	0.83[ASN][1000 genomes]
rs9257269	0.85[ASN][1000 genomes]
rs9257270	0.85[ASN][1000 genomes]
rs9257274	0.86[ASN][1000 genomes]
rs9257280	0.87[ASN][1000 genomes]
rs9257281	0.88[ASN][1000 genomes]
rs9257328	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9257395	0.82[ASN][1000 genomes]
rs9257425	0.81[EUR][1000 genomes]
rs929042	0.91[ASN][1000 genomes]
rs9368576	0.81[ASN][1000 genomes]
rs9378149	0.81[ASN][1000 genomes]
rs9393932	0.81[ASN][1000 genomes]
rs9393933	0.81[ASN][1000 genomes]
rs9404976	0.81[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28862800-28864600	Active TSS	Monocytes-CD14+_RO01746	blood
2	chr6:28862800-28864800	Active TSS	Fetal Brain Female	brain
3	chr6:28862800-28865200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28862800-28865200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:28862800-28865200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr6:28862800-28865400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:28862800-28866000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:28862800-28866200	Active TSS	Fetal Stomach	stomach
9	chr6:28862800-28866200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:28862800-28866400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:28862800-28866400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:28862800-28866400	Active TSS	Fetal Lung	lung
13	chr6:28863000-28863600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr6:28863000-28863600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:28863000-28864000	Active TSS	Right Atrium	heart
16	chr6:28863000-28864400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:28863000-28864600	Active TSS	Primary monocytes fromperipheralblood	blood
18	chr6:28863000-28864600	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr6:28863000-28864600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:28863000-28864600	Active TSS	Fetal Brain Male	brain
21	chr6:28863000-28864800	Active TSS	Primary B cells from peripheral blood	blood
22	chr6:28863000-28864800	Active TSS	Primary T cells from cord blood	blood
23	chr6:28863000-28864800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:28863000-28865000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:28863000-28865000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:28863000-28865000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:28863000-28865000	Active TSS	Brain Anterior Caudate	brain
28	chr6:28863000-28865000	Active TSS	Stomach Mucosa	stomach
29	chr6:28863000-28865200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:28863000-28865200	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr6:28863000-28865200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr6:28863000-28865200	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr6:28863000-28865200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:28863000-28865200	Active TSS	Adipose Nuclei	Adipose
35	chr6:28863000-28865200	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:28863000-28865200	Active TSS	Colonic Mucosa	Colon
37	chr6:28863000-28865200	Active TSS	Colon Smooth Muscle	Colon
38	chr6:28863000-28865200	Active TSS	Duodenum Mucosa	Duodenum
39	chr6:28863000-28865200	Active TSS	Fetal Heart	heart
40	chr6:28863000-28865200	Active TSS	Fetal Intestine Large	intestine
41	chr6:28863000-28865200	Active TSS	Placenta Amnion	Placenta Amnion
42	chr6:28863000-28865200	Active TSS	Rectal Smooth Muscle	rectum
43	chr6:28863000-28865200	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr6:28863000-28865200	Active TSS	Thymus	Thymus
45	chr6:28863000-28865200	Active TSS	GM12878-XiMat	blood
46	chr6:28863000-28865200	Active TSS	NH-A	brain
47	chr6:28863000-28865400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:28863000-28865400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:28863000-28865400	Active TSS	Aorta	Aorta
50	chr6:28863000-28865400	Active TSS	Brain Angular Gyrus	brain

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