Variant report

Variant	rs6689656
Chromosome Location	chr1:155991046-155991047
allele	C/G
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	POLR2A	chr1:155990086-155991082	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr1:155990502-155991059	K562	blood:	n/a	n/a
3	TCF7L2	chr1:155990581-155991128	HCT-116	colon:	n/a	chr1:155990825-155990839
4	POLR2A	chr1:155990506-155991100	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:155989977-155991109	K562	blood:	n/a	n/a
6	POLR2A	chr1:155990329-155991072	Hela-S3	cervix:	n/a	n/a
7	GABPA	chr1:155990345-155991208	A549	lung:	n/a	n/a
8	POLR2A	chr1:155990489-155991091	SK-N-MC	brain:	n/a	n/a
9	GTF2F1	chr1:155990596-155991126	Hela-S3	cervix:	n/a	n/a
10	CREB1	chr1:155990361-155991055	HepG2	liver:	n/a	n/a
11	ATF2	chr1:155990557-155991058	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:155990430-155991057	K562	blood:	n/a	n/a
13	ELK4	chr1:155990574-155991056	Hela-S3	cervix:	n/a	chr1:155990743-155990752 chr1:155990759-155990770 chr1:155990742-155990753 chr1:155990743-155990751
14	GABPA	chr1:155990506-155991100	HL-60	blood:	n/a	n/a
15	ETS1	chr1:155990370-155991064	A549	lung:	n/a	chr1:155990743-155990752 chr1:155990743-155990752 chr1:155990743-155990752 chr1:155990794-155990807 chr1:155990793-155990806 chr1:155990795-155990802 chr1:155990743-155990752 chr1:155990743-155990752 chr1:155990739-155990755
16	ELF1	chr1:155990304-155991077	MCF-7	breast:	n/a	chr1:155990739-155990752 chr1:155990711-155990724
17	SIX5	chr1:155990434-155991212	A549	lung:	n/a	chr1:155990796-155990805 chr1:155990794-155990803
18	TAF1	chr1:155990500-155991085	ECC-1	luminal epithelium:	n/a	n/a
19	GABPA	chr1:155990233-155991068	K562	blood:	n/a	n/a
20	HCFC1	chr1:155989673-155991438	Hela-S3	cervix:	n/a	n/a
21	ELF1	chr1:155990309-155991170	HCT-116	colon:	n/a	chr1:155990739-155990752 chr1:155990711-155990724
22	GABPA	chr1:155990374-155991205	SK-N-SH	brain:	n/a	n/a
23	TCF7L2	chr1:155990577-155991261	MCF-7	breast:	n/a	chr1:155991148-155991157 chr1:155990825-155990839 chr1:155991147-155991156 chr1:155991144-155991160 chr1:155991148-155991155
24	TCF7L2	chr1:155990536-155991228	Hela-S3	cervix:	n/a	chr1:155991148-155991157 chr1:155990825-155990839 chr1:155991147-155991156 chr1:155991144-155991160 chr1:155991148-155991155
25	POLR2A	chr1:155989685-155991165	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr1:155990040-155991119	SK-N-SH	brain:	n/a	n/a
27	ELF1	chr1:155990374-155991084	SK-N-SH	brain:	n/a	chr1:155990739-155990752 chr1:155990711-155990724
28	REST	chr1:155989779-155991329	H1-neurons	neurons:	n/a	chr1:155990023-155990030
29	POLR2A	chr1:155990061-155991065	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr1:155990305-155991063	HUVEC	blood vessel:	n/a	n/a
31	TCF12	chr1:155990504-155991069	ECC-1	luminal epithelium:	n/a	chr1:155990953-155990960
32	ETS1	chr1:155990458-155991063	K562	blood:	n/a	chr1:155990743-155990752 chr1:155990743-155990752 chr1:155990743-155990752 chr1:155990794-155990807 chr1:155990793-155990806 chr1:155990795-155990802 chr1:155990743-155990752 chr1:155990743-155990752 chr1:155990739-155990755
33	POLR2A	chr1:155990480-155991067	GM12891	blood:	n/a	n/a
34	PML	chr1:155990346-155991123	GM12878	blood:	n/a	n/a
35	GABPA	chr1:155990360-155991058	MCF-7	breast:	n/a	n/a
36	POLR2A	chr1:155990211-155991120	H1-neurons	neurons:	n/a	n/a
37	TCF7L2	chr1:155990530-155991282	Hela-S3	cervix:	n/a	chr1:155991148-155991157 chr1:155990825-155990839 chr1:155991147-155991156 chr1:155991144-155991160 chr1:155991148-155991155
38	GABPA	chr1:155990044-155991411	MCF-7	breast:	n/a	n/a
39	GABPA	chr1:155990391-155991161	HL-60	blood:	n/a	n/a
40	GABPA	chr1:155990239-155991126	A549	lung:	n/a	n/a
41	POLR2A	chr1:155990185-155991119	PFSK-1	brain:	n/a	n/a
42	TCF7L2	chr1:155990560-155991278	PANC-1	pancreas:	n/a	chr1:155991148-155991157 chr1:155990825-155990839 chr1:155991147-155991156 chr1:155991144-155991160 chr1:155991148-155991155
43	POLR2A	chr1:155990328-155991183	SK-N-MC	brain:	n/a	n/a
44	TCF7L2	chr1:155990198-155991283	HEK293	kidney:	n/a	chr1:155991148-155991157 chr1:155990825-155990839 chr1:155991147-155991156 chr1:155991144-155991160 chr1:155991148-155991155
45	ELF1	chr1:155990357-155991168	HCT-116	colon:	n/a	chr1:155990739-155990752 chr1:155990711-155990724
46	GABPA	chr1:155990498-155991119	SK-N-SH	brain:	n/a	n/a
47	HCFC1	chr1:155990545-155991056	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155989323..155991175-chr1:156023059..156025396,2	K562	blood:
2	chr1:155987340..155997180-chr1:156020881..156026682,16	K562	blood:
3	chr1:155971547..155973153-chr1:155989998..155991743,2	MCF-7	breast:
4	chr1:155989282..155991802-chr1:156050650..156052528,3	MCF-7	breast:
5	chr1:155947943..155949602-chr1:155989760..155992633,2	MCF-7	breast:
6	chr1:155902986..155905727-chr1:155989614..155992044,2	MCF-7	breast:
7	chr1:155989047..155993552-chr1:156021675..156026301,17	MCF-7	breast:
8	chr1:155990547..155991212-chr1:156030604..156031228,2	MCF-7	breast:
9	chr1:155990076..155992567-chr1:156083817..156085926,2	MCF-7	breast:
10	chr1:155990929..155994838-chr1:156000466..156003065,3	K562	blood:
11	chr1:155989866..155991878-chr20:57465038..57467717,2	MCF-7	breast:
12	chr1:155902135..155904272-chr1:155989311..155991298,2	MCF-7	breast:
13	chr1:155988173..156003032-chr1:156020965..156026206,23	MCF-7	breast:
14	chr1:155902926..155905486-chr1:155988342..155992219,3	K562	blood:
15	chr1:155947462..155948981-chr1:155988389..155991184,2	K562	blood:
16	chr1:155902781..155905486-chr1:155988342..155993651,4	K562	blood:
17	chr1:155970847..155975108-chr1:155988635..155992129,4	MCF-7	breast:

Variant related genes	Relation type
SSR2	TF binding region
ENSG00000116586	Chromatin interaction
ENSG00000087460	Chromatin interaction
ENSG00000273002	Chromatin interaction
ENSG00000132698	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000254726	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000160789	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1003725	1.00[AMR][1000 genomes]
rs57110733	1.00[AMR][1000 genomes]
rs57875392	1.00[AMR][1000 genomes]
rs59293055	1.00[AMR][1000 genomes]
rs60243295	1.00[AMR][1000 genomes]
rs60291493	1.00[AMR][1000 genomes]
rs61290992	1.00[AMR][1000 genomes]
rs6685797	1.00[AMR][1000 genomes]
rs73001016	1.00[AMR][1000 genomes]
rs73001054	1.00[AMR][1000 genomes]
rs73001080	1.00[AMR][1000 genomes]
rs73001081	1.00[AMR][1000 genomes]
rs73001083	1.00[AMR][1000 genomes]
rs73001085	1.00[AMR][1000 genomes]
rs73001088	1.00[AMR][1000 genomes]
rs73001099	1.00[AMR][1000 genomes]
rs73002905	1.00[AMR][1000 genomes]
rs73002907	1.00[AMR][1000 genomes]
rs73002917	1.00[AMR][1000 genomes]
rs73002929	1.00[AMR][1000 genomes]
rs73002930	1.00[AMR][1000 genomes]
rs73004969	1.00[AMR][1000 genomes]
rs7512584	1.00[AMR][1000 genomes]
rs7516232	1.00[AMR][1000 genomes]
rs7553076	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155989600-155991200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:155989600-155991200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:155989600-155991200	Active TSS	Psoas Muscle	Psoas
4	chr1:155989800-155991200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:155989800-155991200	Active TSS	Right Atrium	heart
6	chr1:155989800-155991200	Active TSS	Right Ventricle	heart
7	chr1:155989800-155991200	Active TSS	HepG2	liver
8	chr1:155990000-155991200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:155990000-155991200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:155990000-155991200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:155990000-155991200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:155990000-155991200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:155990000-155991200	Active TSS	Muscle Satellite Cultured Cells	--
14	chr1:155990000-155991200	Active TSS	Brain Substantia Nigra	brain
15	chr1:155990000-155991200	Active TSS	Fetal Brain Male	brain
16	chr1:155990000-155991200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr1:155990000-155991200	Active TSS	A549	lung
18	chr1:155990000-155991200	Active TSS	Osteobl	bone
19	chr1:155990200-155991200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:155990200-155991200	Active TSS	Fetal Brain Female	brain
21	chr1:155990400-155991200	Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr1:155990400-155991200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:155990400-155991200	Active TSS	Brain Anterior Caudate	brain
24	chr1:155990400-155991200	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr1:155990400-155991200	Active TSS	Rectal Smooth Muscle	rectum
26	chr1:155990400-155991200	Active TSS	Stomach Smooth Muscle	stomach
27	chr1:155990800-155991200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:155990800-155991200	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr1:155990800-155991200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:155990800-155991200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr1:155990800-155991200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:155990800-155991200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr1:155990800-155991200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr1:155990800-155991200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:155990800-155991200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:155990800-155991200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr1:155990800-155991200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:155990800-155991200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr1:155990800-155991200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:155990800-155991200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:155990800-155991200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:155990800-155991200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr1:155990800-155991200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:155990800-155991200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:155990800-155991200	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr1:155990800-155991200	Flanking Active TSS	Liver	Liver
47	chr1:155990800-155991200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr1:155990800-155991200	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr1:155990800-155991200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr1:155990800-155991200	Flanking Active TSS	Fetal Intestine Large	intestine

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