Variant report

Variant	rs2073561
Chromosome Location	chr7:127227769-127227770
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	RCOR1	chr7:127227637-127229436	IMR90	lung:	n/a	n/a
2	MAX	chr7:127227763-127229310	HepG2	liver:	n/a	n/a
3	SMARCB1	chr7:127227767-127229392	Hela-S3	cervix:	n/a	n/a
4	E2F6	chr7:127227747-127229187	K562	blood:	n/a	chr7:127228577-127228585 chr7:127228234-127228249 chr7:127227854-127227863 chr7:127228938-127228953
5	RCOR1	chr7:127227769-127229284	K562	blood:	n/a	n/a
6	SMC3	chr7:127227447-127229528	SK-N-SH	brain:	n/a	chr7:127229017-127229027 chr7:127228184-127228194
7	CTCF	chr7:127227682-127229461	A549	lung:	n/a	chr7:127229014-127229027
8	CBX3	chr7:127227536-127229310	K562	blood:	n/a	n/a
9	POLR2A	chr7:127227695-127229210	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr7:127227455-127229197	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr7:127227726-127227813	HepG2	liver:	n/a	n/a
12	HMGN3	chr7:127227753-127227868	K562	blood:	n/a	n/a
13	POLR2A	chr7:127227697-127227830	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr7:127227689-127229609	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr7:127227510-127229573	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:127226810..127231119-chr7:127290066..127293801,4	MCF-7	breast:
2	chr7:127030656..127034603-chr7:127225190..127230310,7	MCF-7	breast:
3	chr7:127029421..127032644-chr7:127225849..127230043,4	K562	blood:
4	chr7:127226125..127229974-chr7:127289784..127293571,8	MCF-7	breast:
5	chr7:127223375..127232960-chr7:127286940..127295803,24	K562	blood:
6	chr7:127030702..127032822-chr7:127225677..127228410,2	K562	blood:
7	chr7:127222868..127230871-chr7:127290370..127294912,16	K562	blood:

Variant related genes	Relation type
GCC1	TF binding region
FSCN3	TF binding region
ARF5	TF binding region
ENSG00000048405	Chromatin interaction
ENSG00000197157	Chromatin interaction
ENSG00000240790	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1090682	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1090683	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12536382	0.85[CHB][hapmap]
rs12671806	1.00[YRI][hapmap]
rs2582717	0.81[CEU][hapmap]
rs327510	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs327511	0.82[EUR][1000 genomes]
rs327512	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs327516	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs327521	0.81[EUR][1000 genomes]
rs3735642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757793	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55791028	0.84[ASN][1000 genomes]
rs594141	0.87[EUR][1000 genomes]
rs62481355	0.84[ASN][1000 genomes]
rs67719649	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs698406	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs712697	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs712698	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs712699	0.83[EUR][1000 genomes]
rs712700	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs712701	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs712703	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs712704	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72607743	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs806175	0.81[CEU][hapmap]
rs806192	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs806193	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs806195	0.84[EUR][1000 genomes]
rs806196	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs806214	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs806215	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs806216	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs806218	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs806219	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127226000-127227800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:127226000-127227800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:127226000-127228000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:127226000-127228000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:127226200-127227800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:127226200-127227800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:127226200-127227800	Weak transcription	Aorta	Aorta
8	chr7:127226200-127227800	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr7:127226200-127227800	Weak transcription	Colonic Mucosa	Colon
10	chr7:127226200-127227800	Weak transcription	Esophagus	oesophagus
11	chr7:127226200-127227800	Weak transcription	Fetal Brain Female	brain
12	chr7:127226200-127227800	Weak transcription	Fetal Thymus	thymus
13	chr7:127226200-127227800	Weak transcription	Gastric	stomach
14	chr7:127226200-127227800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:127226200-127227800	Weak transcription	Right Atrium	heart
16	chr7:127226200-127227800	Weak transcription	Spleen	Spleen
17	chr7:127226200-127227800	Weak transcription	HSMMtube	muscle
18	chr7:127226200-127227800	Weak transcription	NH-A	brain
19	chr7:127226200-127227800	Weak transcription	NHDF-Ad	bronchial
20	chr7:127226200-127228000	Weak transcription	Small Intestine	intestine
21	chr7:127226400-127227800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:127226400-127227800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:127226400-127227800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr7:127226400-127227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:127226400-127227800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:127226400-127227800	Weak transcription	Brain Germinal Matrix	brain
27	chr7:127226400-127227800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:127226400-127227800	Weak transcription	Fetal Brain Male	brain
29	chr7:127226400-127227800	Weak transcription	Fetal Lung	lung
30	chr7:127226400-127227800	Weak transcription	A549	lung
31	chr7:127226400-127227800	Weak transcription	Hela-S3	cervix
32	chr7:127226400-127228800	Weak transcription	Fetal Heart	heart
33	chr7:127227000-127227800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:127227400-127227800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr7:127227400-127227800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr7:127227400-127227800	Enhancers	Primary B cells from peripheral blood	blood
37	chr7:127227400-127227800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr7:127227400-127227800	Enhancers	Brain Angular Gyrus	brain
39	chr7:127227400-127227800	Enhancers	Brain Substantia Nigra	brain
40	chr7:127227400-127227800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr7:127227400-127227800	Enhancers	Fetal Muscle Leg	muscle
42	chr7:127227400-127227800	Enhancers	Placenta Amnion	Placenta Amnion
43	chr7:127227400-127227800	Enhancers	HMEC	breast
44	chr7:127227400-127227800	Enhancers	NHEK	skin
45	chr7:127227600-127227800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr7:127227600-127227800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr7:127227600-127227800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:127227600-127227800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
49	chr7:127227600-127227800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr7:127227600-127227800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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