Variant report

Variant	rs28431418
Chromosome Location	chr4:3075588-3075589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:183)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:183 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:3075494-3075772	U87	brain:	n/a	n/a
2	E2F6	chr4:3075531-3075771	K562	blood:	n/a	n/a
3	SP1	chr4:3075361-3075836	HepG2	liver:	n/a	chr4:3075447-3075457 chr4:3075447-3075456
4	POLR2A	chr4:3075450-3075878	GM12878	blood:	n/a	n/a
5	SP1	chr4:3075491-3075840	GM12878	blood:	n/a	n/a
6	MXI1	chr4:3075132-3076606	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:3075416-3075920	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr4:3075428-3075825	GM12878	blood:	n/a	n/a
9	POLR2A	chr4:3075449-3075846	GM12892	blood:	n/a	n/a
10	TCF3	chr4:3075475-3075756	GM12878	blood:	n/a	chr4:3075552-3075566
11	POLR2A	chr4:3075066-3078105	GM15510	blood:	n/a	n/a
12	POLR2A	chr4:3075339-3076734	MCF-7	breast:	n/a	n/a
13	TAL1	chr4:3075536-3075697	K562	blood:	n/a	n/a
14	MXI1	chr4:3075478-3075678	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:3075444-3075761	Hela-S3	cervix:	n/a	n/a
16	ZKSCAN1	chr4:3075526-3075627	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr4:3075378-3075885	ProgFib	skin:	n/a	n/a
18	ZBTB7A	chr4:3075021-3075688	K562	blood:	n/a	chr4:3075182-3075189
19	CREB1	chr4:3075553-3075808	A549	lung:	n/a	n/a
20	MXI1	chr4:3074910-3076677	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr4:3075500-3075818	HUVEC	blood vessel:	n/a	n/a
22	CREB1	chr4:3075473-3076678	K562	blood:	n/a	n/a
23	YY1	chr4:3075548-3075786	GM12891	blood:	n/a	n/a
24	MAZ	chr4:3075228-3076619	K562	blood:	n/a	n/a
25	POLR2A	chr4:3075445-3075769	GM12892	blood:	n/a	n/a
26	POLR2A	chr4:3075327-3080089	GM18505	blood:	n/a	n/a
27	RCOR1	chr4:3075296-3075805	K562	blood:	n/a	n/a
28	POLR2A	chr4:3075306-3075786	U87	brain:	n/a	n/a
29	SP1	chr4:3075387-3076643	HCT-116	colon:	n/a	chr4:3075447-3075457 chr4:3076267-3076276 chr4:3076265-3076276 chr4:3075447-3075456
30	YY1	chr4:3075486-3075819	K562	blood:	n/a	n/a
31	MAZ	chr4:3075379-3076478	HepG2	liver:	n/a	n/a
32	ZBTB7A	chr4:3075091-3076165	K562	blood:	n/a	chr4:3075182-3075189
33	CREB1	chr4:3075492-3076737	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:3075430-3075786	SK-N-SH	brain:	n/a	n/a
35	E2F6	chr4:3075463-3075934	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr4:3075427-3075880	HEK293	kidney:	n/a	n/a
37	ZBTB7A	chr4:3074957-3075883	ECC-1	luminal epithelium:	n/a	chr4:3075182-3075189
38	POLR2A	chr4:3075519-3075783	Hela-S3	cervix:	n/a	n/a
39	HEY1	chr4:3075354-3075804	HepG2	liver:	n/a	n/a
40	CUX1	chr4:3075564-3075687	K562	blood:	n/a	n/a
41	HEY1	chr4:3075471-3075765	K562	blood:	n/a	n/a
42	POLR2A	chr4:3075338-3075826	K562	blood:	n/a	n/a
43	POLR2A	chr4:3075279-3075868	H1-hESC	embryonic stem cell:	n/a	n/a
44	E2F6	chr4:3075518-3075823	K562	blood:	n/a	n/a
45	JUND	chr4:3075557-3075676	K562	blood:	n/a	n/a
46	MAX	chr4:3075433-3075826	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr4:3075449-3075935	GM12892	blood:	n/a	n/a
48	E2F6	chr4:3075481-3075866	A549	lung:	n/a	n/a
49	POLR2A	chr4:3075341-3075834	HepG2	liver:	n/a	n/a
50	MXI1	chr4:3075512-3075776	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:3074016..3078502-chr4:3111809..3117809,7	MCF-7	breast:
2	chr17:16556241..16557924-chr4:3075466..3077603,2	MCF-7	breast:
3	chr4:3068906..3071079-chr4:3073190..3075687,2	MCF-7	breast:
4	chr4:3074885..3077461-chr4:3292207..3294882,2	MCF-7	breast:
5	chr4:2964356..2966158-chr4:3074837..3077632,2	K562	blood:
6	chr4:2262471..2264332-chr4:3074788..3077577,2	MCF-7	breast:
7	chr4:2468745..2470693-chr4:3075535..3077781,3	K562	blood:

No data

Variant related genes	Relation type
HTT	TF binding region
ENSG00000125388	Chromatin interaction
ENSG00000264765	Chromatin interaction
ENSG00000159788	Chromatin interaction
ENSG00000197386	Chromatin interaction
ENSG00000063978	Chromatin interaction
ENSG00000197566	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000123933	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10011412	0.95[EUR][1000 genomes]
rs61792464	0.84[AFR][1000 genomes]
rs9291159	0.93[EUR][1000 genomes]
rs9993542	0.96[EUR][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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv3326369	chr4:3074679-3077527	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv3406168	chr4:3075379-3078127	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3074800-3075600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:3074800-3075600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr4:3074800-3075600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:3074800-3075600	Enhancers	Spleen	Spleen
5	chr4:3074800-3075600	Flanking Active TSS	HepG2	liver
6	chr4:3074800-3075800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:3074800-3076400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:3074800-3077600	Active TSS	Fetal Brain Female	brain
9	chr4:3074800-3078600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr4:3075000-3075600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr4:3075000-3075600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr4:3075000-3075600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:3075000-3075600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:3075000-3075600	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr4:3075000-3075600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr4:3075000-3075600	Enhancers	Fetal Brain Male	brain
17	chr4:3075000-3075600	Flanking Active TSS	Fetal Muscle Trunk	muscle
18	chr4:3075000-3075600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
19	chr4:3075000-3075600	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr4:3075000-3075600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr4:3075000-3075800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr4:3075000-3075800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:3075000-3075800	Flanking Active TSS	Dnd41	blood
24	chr4:3075000-3076400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:3075000-3076600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:3075000-3077000	Active TSS	Osteobl	bone
27	chr4:3075000-3077400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:3075000-3077400	Active TSS	HSMM	muscle
29	chr4:3075000-3077600	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr4:3075000-3077600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr4:3075000-3077600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr4:3075000-3077600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:3075000-3077600	Active TSS	Brain Germinal Matrix	brain
34	chr4:3075000-3077800	Active TSS	H9 Cell Line	embryonic stem cell
35	chr4:3075000-3078400	Active TSS	A549	lung
36	chr4:3075200-3075600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:3075200-3075600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr4:3075200-3075600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr4:3075200-3075600	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr4:3075200-3075600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr4:3075200-3075600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:3075200-3075600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr4:3075200-3075600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr4:3075200-3075600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:3075200-3075600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr4:3075200-3075600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:3075200-3075600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr4:3075200-3075600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:3075200-3075600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:3075200-3075600	Flanking Active TSS	Adipose Nuclei	Adipose

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