Variant report

Variant	rs6940553
Chromosome Location	chr6:25035888-25035889
allele	G/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	GATA1	chr6:25035578-25036794	K562	blood:	n/a	chr6:25035907-25035916 chr6:25036078-25036089
2	MTA3	chr6:25035868-25036460	GM12878	blood:	n/a	n/a
3	BHLHE40	chr6:25035572-25036590	GM12878	blood:	n/a	n/a
4	BHLHE40	chr6:25035708-25036602	K562	blood:	n/a	n/a
5	POLR2A	chr6:25035506-25036091	GM12892	blood:	n/a	n/a
6	RCOR1	chr6:25035779-25036719	K562	blood:	n/a	n/a
7	RUNX3	chr6:25035565-25036538	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:25034725-25036865	PBDE	blood:	n/a	n/a
9	RUNX3	chr6:25035503-25036050	GM12878	blood:	n/a	n/a
10	NFYB	chr6:25035596-25036044	GM12878	blood:	n/a	n/a
11	GATA1	chr6:25035662-25037146	PBDE	blood:	n/a	chr6:25035907-25035916 chr6:25036078-25036089
12	TAL1	chr6:25035830-25036005	K562	blood:	n/a	chr6:25035909-25035917
13	TEAD4	chr6:25035592-25036082	K562	blood:	n/a	n/a
14	PML	chr6:25035447-25036297	GM12878	blood:	n/a	chr6:25035639-25035647
15	WRNIP1	chr6:25035376-25036566	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25028396..25029900-chr6:25034648..25037120,2	K562	blood:

Variant related genes	Relation type
RN7SL334P	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10214565	1.00[EUR][1000 genomes]
rs1172085	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16890115	1.00[EUR][1000 genomes]
rs1880273	1.00[EUR][1000 genomes]
rs554473	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58400813	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60614435	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6904367	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73388152	1.00[EUR][1000 genomes]
rs73388164	1.00[EUR][1000 genomes]
rs7765755	0.83[AMR][1000 genomes];1.00[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	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25028200-25037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25034400-25036400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr6:25034600-25036000	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr6:25034600-25036200	Active TSS	Colonic Mucosa	Colon
5	chr6:25034600-25036400	Flanking Active TSS	Primary B cells from peripheral blood	blood
6	chr6:25034600-25036400	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr6:25034600-25036400	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr6:25034600-25036400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:25034600-25036400	Active TSS	Duodenum Mucosa	Duodenum
10	chr6:25034600-25036400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr6:25034600-25036400	Enhancers	Fetal Intestine Large	intestine
12	chr6:25034600-25036400	Enhancers	Fetal Intestine Small	intestine
13	chr6:25034600-25036400	Flanking Active TSS	Thymus	Thymus
14	chr6:25034600-25036600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:25034600-25036600	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr6:25034600-25036600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr6:25034600-25036600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:25034600-25036600	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr6:25034600-25036600	Flanking Active TSS	GM12878-XiMat	blood
20	chr6:25034600-25036800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr6:25034600-25036800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr6:25034600-25036800	Flanking Active TSS	Dnd41	blood
23	chr6:25034600-25037200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:25034600-25038600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:25034800-25036000	Active TSS	Brain Hippocampus Middle	brain
26	chr6:25034800-25036200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr6:25034800-25037200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:25035000-25036000	Active TSS	Rectal Smooth Muscle	rectum
29	chr6:25035000-25036400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr6:25035000-25036400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr6:25035000-25036400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr6:25035000-25036600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr6:25035000-25037000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:25035000-25037400	Enhancers	K562	blood
35	chr6:25035200-25036200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:25035200-25036200	Enhancers	Fetal Muscle Leg	muscle
37	chr6:25035200-25036200	Enhancers	HSMMtube	muscle
38	chr6:25035200-25036400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:25035200-25036400	Enhancers	Brain Anterior Caudate	brain
40	chr6:25035200-25036600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr6:25035200-25036600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr6:25035200-25041200	Weak transcription	Fetal Kidney	kidney
43	chr6:25035200-25044600	Weak transcription	Right Atrium	heart
44	chr6:25035400-25036200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:25035400-25036600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:25035600-25036000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:25035600-25036000	Enhancers	Gastric	stomach
48	chr6:25035600-25036000	Enhancers	Lung	lung
49	chr6:25035600-25036000	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr6:25035600-25036000	Flanking Active TSS	Stomach Smooth Muscle	stomach

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