Variant report

Variant	rs58985578
Chromosome Location	chr6:20211277-20211278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr6:20211119-20213474	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:20211023-20211967	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:20211253-20213604	GM19193	blood:	n/a	n/a
4	FOXA1	chr6:20211207-20211704	T-47D	breast:	n/a	n/a
5	NFYB	chr6:20211219-20211701	GM12878	blood:	n/a	chr6:20211581-20211596
6	CHD2	chr6:20211265-20211948	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOXA1	chr6:20211160-20211652	T-47D	breast:	n/a	n/a
8	SIN3A	chr6:20211276-20213501	H1-hESC	embryonic stem cell:	n/a	chr6:20212668-20212677
9	MAX	chr6:20211266-20211567	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZEB1	chr6:20211178-20211587	GM12878	blood:	n/a	n/a
11	TEAD4	chr6:20211170-20214290	K562	blood:	n/a	n/a
12	POLR2A	chr6:20211128-20214212	MCF10A-Er-Src	breast:	n/a	n/a
13	ZNF263	chr6:20211089-20213480	HEK293-T-REx	kidney:	n/a	chr6:20212781-20212790 chr6:20212936-20212945 chr6:20211765-20211774 chr6:20211465-20211486
14	POLR2A	chr6:20211138-20213934	GM12891	blood:	n/a	n/a
15	NR2F2	chr6:20211181-20211889	K562	blood:	n/a	n/a
16	POLR2A	chr6:20211156-20213720	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:20211137-20214191	PBDE	blood:	n/a	n/a
18	MAX	chr6:20211206-20211524	GM12878	blood:	n/a	n/a
19	SMC3	chr6:20211268-20213479	Hela-S3	cervix:	n/a	chr6:20213136-20213143 chr6:20212987-20212997 chr6:20212886-20212896 chr6:20212896-20212906
20	CTCF	chr6:20211245-20213624	A549	lung:	n/a	chr6:20212886-20212899 chr6:20212998-20213016 chr6:20212911-20212924
21	POLR2A	chr6:20211195-20211999	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:52840503..52842605-chr6:20208710..20211532,2	MCF-7	breast:
2	chr6:20207945..20211455-chr6:26105249..26107952,3	MCF-7	breast:
3	chr6:20208250..20214334-chr6:20400294..20406447,14	K562	blood:
4	chr6:20126269..20128367-chr6:20209873..20212157,2	MCF-7	breast:
5	chr6:20209069..20211986-chr6:20231381..20233005,2	K562	blood:
6	chr2:25300005..25301584-chr6:20210003..20211589,2	MCF-7	breast:
7	chr6:17393765..17396443-chr6:20210532..20213161,2	MCF-7	breast:
8	chr6:20208632..20214725-chr6:20400593..20405219,15	K562	blood:
9	chr6:20208057..20215931-chr6:20401288..20405953,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227803	TF binding region
ENSG00000112242	Chromatin interaction
ENSG00000112186	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2328392	0.93[AFR][1000 genomes]
rs61737148	0.99[AFR][1000 genomes]
rs62397953	0.90[EUR][1000 genomes]
rs62397955	0.90[EUR][1000 genomes]
rs7758980	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029729	chr6:20113226-20235122	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538155	chr6:20113226-20235122	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1027355	chr6:20207893-20261048	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:20206800-20211400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:20207600-20211400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:20210000-20211400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:20210000-20211600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr6:20210000-20212200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:20210200-20212000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:20210200-20213200	Active TSS	Duodenum Mucosa	Duodenum
8	chr6:20210600-20211400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:20210600-20211400	Enhancers	Aorta	Aorta
10	chr6:20210600-20211800	Enhancers	Brain Germinal Matrix	brain
11	chr6:20210600-20213600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:20210600-20213800	Active TSS	Ovary	ovary
13	chr6:20210800-20211400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr6:20210800-20211400	Active TSS	Fetal Stomach	stomach
15	chr6:20210800-20211600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr6:20210800-20213000	Active TSS	Fetal Intestine Small	intestine
17	chr6:20211000-20211400	Enhancers	Primary B cells from cord blood	blood
18	chr6:20211000-20211400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:20211000-20211400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:20211000-20211400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr6:20211000-20211400	Enhancers	Right Ventricle	heart
22	chr6:20211000-20211400	Flanking Active TSS	NHEK	skin
23	chr6:20211000-20211600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:20211000-20211600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:20211000-20211600	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr6:20211000-20211800	Enhancers	Primary T cells from cord blood	blood
27	chr6:20211000-20211800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:20211000-20212000	Flanking Active TSS	Dnd41	blood
29	chr6:20211000-20212600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:20211000-20213200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr6:20211000-20213200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:20211000-20213200	Active TSS	Fetal Intestine Large	intestine
33	chr6:20211000-20213400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:20211000-20213400	Active TSS	GM12878-XiMat	blood
35	chr6:20211000-20213600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr6:20211000-20213600	Active TSS	H9 Cell Line	embryonic stem cell
37	chr6:20211000-20213600	Active TSS	Right Atrium	heart
38	chr6:20211200-20211400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:20211200-20211400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:20211200-20211400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:20211200-20211400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:20211200-20211400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
43	chr6:20211200-20211400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:20211200-20211400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:20211200-20211400	Enhancers	Fetal Muscle Leg	muscle
46	chr6:20211200-20211400	Enhancers	Placenta	Placenta
47	chr6:20211200-20211400	Flanking Active TSS	Pancreas	Pancrea
48	chr6:20211200-20211400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr6:20211200-20211400	Flanking Active TSS	Stomach Mucosa	stomach
50	chr6:20211200-20211400	Flanking Active TSS	HMEC	breast

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