Variant report

Variant	rs2267635
Chromosome Location	chr6:29592431-29592432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:29592083-29592593	H1-neurons	neurons:	n/a	n/a
2	EGR1	chr6:29592226-29592643	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF263	chr6:29592218-29592795	HEK293-T-REx	kidney:	n/a	chr6:29592419-29592440 chr6:29592593-29592602 chr6:29592576-29592585
4	GTF2F1	chr6:29592295-29592459	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZC3H11A	chr6:29592431-29592547	K562	blood:	n/a	n/a
6	POLR2A	chr6:29592125-29592990	H1-neurons	neurons:	n/a	n/a
7	REST	chr6:29591706-29593872	H1-neurons	neurons:	n/a	n/a
8	HDAC2	chr6:29592149-29592579	H1-hESC	embryonic stem cell:	n/a	chr6:29592558-29592572 chr6:29592538-29592547
9	CTCF	chr6:29592360-29592510	HRE	kidney:	n/a	n/a
10	CTBP2	chr6:29591778-29593391	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:29592057-29592546	PFSK-1	brain:	n/a	n/a
12	SIN3AK20	chr6:29592220-29592569	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr6:29592172-29592716	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3A	chr6:29592032-29593201	H1-hESC	embryonic stem cell:	n/a	chr6:29592372-29592383

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29592381-29592431	Hepatocyte	liver:	n/a
2	chr6:29592381-29592431	HCPEpiC	choroid plexus:	n/a
3	chr6:29592381-29592431	SK-N-SH	brain:	n/a
4	chr6:29592381-29592431	HUVEC	blood vessel:	n/a
5	chr6:29592381-29592431	SKMC	muscle:	n/a
6	chr6:29592381-29592431	GM12891	blood:	n/a
7	chr6:29592381-29592431	SK-N-MC	brain:	n/a
8	chr6:29592381-29592431	PANC-1	pancreas:	n/a
9	chr6:29592381-29592431	LNCaP	prostate:	n/a
10	chr6:29592381-29592431	Hela-S3	cervix:	n/a
11	chr6:29592381-29592431	HCM	heart:	n/a
12	chr6:29592381-29592431	NB4	blood:	n/a
13	chr6:29592381-29592431	SK-N-SH_RA	brain:	n/a
14	chr6:29592381-29592431	GM12892	blood:	n/a
15	chr6:29592381-29592431	GM12878	blood:	n/a
16	chr6:29592381-29592431	HRPEpiC	eye:	n/a
17	chr6:29592381-29592431	Jurkat	blood:	n/a
18	chr6:29592381-29592431	BE2_C	brain:	n/a
19	chr6:29592381-29592431	ProgFib	skin:	n/a
20	chr6:29592381-29592431	AG04450	lung:	fetal
21	chr6:29592381-29592431	HNPCEpiC	eye:	n/a
22	chr6:29592381-29592431	NT2-D1	testis:	n/a
23	chr6:29592381-29592431	BJ	skin:	n/a
24	chr6:29592381-29592431	GM19239	blood:	n/a
25	chr6:29592381-29592431	A549	lung:	n/a
26	chr6:29592381-29592431	ECC-1	luminal epithelium:	n/a
27	chr6:29592381-29592431	U87	brain:	n/a
28	chr6:29592381-29592431	HCF	heart:	n/a
29	chr6:29592381-29592431	NH-A	brain:	n/a
30	chr6:29592381-29592431	AG09319	gingival:	n/a
31	chr6:29592381-29592431	K562	blood:	n/a
32	chr6:29592381-29592431	T-47D	breast:	n/a
33	chr6:29592381-29592431	HEK293	kidney:	embryo
34	chr6:29592381-29592431	HL-60	blood:	n/a
35	chr6:29592381-29592431	MCF10A-Er-Src	breast:	n/a
36	chr6:29592381-29592431	MCF-7	breast:	n/a
37	chr6:29592381-29592431	NHBE	bronchial:	n/a
38	chr6:29592381-29592431	ovcar-3	ovarian:	n/a
39	chr6:29592381-29592431	GM06990	blood:	n/a
40	chr6:29592381-29592431	HCT-116	colon:	n/a
41	chr6:29592381-29592431	AG09309	skin:	n/a
42	chr6:29592381-29592431	AG10803	skin:	n/a
43	chr6:29592381-29592431	AG04449	skin:	fetal
44	chr6:29592381-29592431	SAEC	small airway:	n/a
45	chr6:29592381-29592431	NHDF-neo	bronchial:	n/a
46	chr6:29592381-29592431	AoSMC	blood vessel:	n/a
47	chr6:29592381-29592431	RPTEC	kidney:	n/a
48	chr6:29592381-29592431	HPAEpiC	pulmonary alveolar:	n/a
49	chr6:29592381-29592431	HRCEpiC	kidney:	n/a
50	chr6:29592381-29592431	Caco-2	colon:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29590884..29592838-chr6:29594081..29596574,2	MCF-7	breast:

No data

Variant related genes	Relation type
GABBR1	TF binding region
GABBR1	CpG island
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12524535	0.82[AMR][1000 genomes]
rs12525400	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528017	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17178028	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28893512	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28893514	0.81[EUR][1000 genomes]
rs28893515	0.81[EUR][1000 genomes]
rs28893516	0.81[EUR][1000 genomes]
rs28893517	0.81[EUR][1000 genomes]
rs28986291	0.90[AMR][1000 genomes]
rs28986295	0.81[EUR][1000 genomes]
rs28986296	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28986299	0.86[EUR][1000 genomes]
rs28986301	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28986303	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28986306	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28986307	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28986308	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29242	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29255	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3025645	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3025646	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3025649	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs362521	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828923	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41286283	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41291762	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41291766	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715044	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29566400-29595200	Weak transcription	Right Atrium	heart
2	chr6:29567600-29595400	Weak transcription	A549	lung
3	chr6:29568600-29595200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:29569400-29595600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:29572200-29595600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:29572400-29593000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:29574400-29595400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:29574800-29595000	Weak transcription	Pancreas	Pancrea
9	chr6:29577600-29595400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:29578800-29595200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:29581800-29596000	Weak transcription	Fetal Heart	heart
12	chr6:29582600-29595400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:29585800-29592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:29585800-29592800	Strong transcription	NHEK	skin
15	chr6:29586000-29592600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:29586400-29592800	Weak transcription	Fetal Brain Male	brain
17	chr6:29588000-29592800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:29588600-29593200	Weak transcription	HUVEC	blood vessel
19	chr6:29589000-29593000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:29589200-29595200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:29589200-29595400	Weak transcription	NHDF-Ad	bronchial
22	chr6:29589200-29595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:29589400-29595000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:29589400-29595400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:29589400-29595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:29589400-29595400	Weak transcription	HSMM	muscle
27	chr6:29589600-29594600	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:29589800-29592600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:29589800-29595000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:29590000-29592800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr6:29590200-29592800	Weak transcription	Primary B cells from cord blood	blood
32	chr6:29590200-29595200	Weak transcription	Fetal Kidney	kidney
33	chr6:29590200-29595400	Weak transcription	Esophagus	oesophagus
34	chr6:29590600-29593000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:29590800-29594400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:29590800-29595200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:29591200-29592800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr6:29591200-29595000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:29591200-29595200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:29591400-29592600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:29591400-29592600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:29591400-29594800	Weak transcription	Osteobl	bone
43	chr6:29591400-29595000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:29591400-29595400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:29591600-29592600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:29591600-29592800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr6:29591600-29593400	Weak transcription	Brain Substantia Nigra	brain
48	chr6:29591600-29594600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:29591600-29595000	Weak transcription	Left Ventricle	heart
50	chr6:29591600-29595200	Weak transcription	Lung	lung

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