Variant report

Variant	rs11973952
Chromosome Location	chr7:39995879-39995880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39987907..39993068-chr7:39995715..40000293,13	MCF-7	breast:
2	chr7:39992254..39999333-chr7:39999543..40002599,8	K562	blood:
3	chr7:39995562..39997587-chr7:40034318..40036710,2	MCF-7	breast:
4	chr7:39994702..39997445-chr7:39998087..39999888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065883	Chromatin interaction
ENSG00000259826	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17496116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17496345	0.83[AFR][1000 genomes]
rs17496579	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17496598	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17496641	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17537614	0.83[AMR][1000 genomes]
rs17537760	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17537852	1.00[AFR][1000 genomes]
rs17538209	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39988200-39996200	Active TSS	GM12878-XiMat	blood
2	chr7:39991800-39996200	Weak transcription	Esophagus	oesophagus
3	chr7:39991800-40000200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:39991800-40000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:39991800-40005200	Weak transcription	Lung	lung
6	chr7:39992000-39999200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr7:39992000-40006400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:39992600-40001200	Weak transcription	Placenta	Placenta
9	chr7:39993200-39997200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:39993400-40000000	Weak transcription	Fetal Thymus	thymus
11	chr7:39993400-40001000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:39993600-39996200	Weak transcription	Left Ventricle	heart
13	chr7:39993600-39996200	Weak transcription	Right Ventricle	heart
14	chr7:39993600-39996600	Enhancers	Liver	Liver
15	chr7:39993600-39999800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr7:39993600-40000000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr7:39993600-40048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:39993800-39997600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:39993800-40000000	Weak transcription	HSMMtube	muscle
20	chr7:39993800-40000800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:39993800-40000800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:39994000-40000800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr7:39994200-39996200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:39994200-39997000	Weak transcription	NHLF	lung
25	chr7:39994200-39997200	Enhancers	Duodenum Mucosa	Duodenum
26	chr7:39994200-39998000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr7:39994200-39999400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:39994200-40008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:39994200-40027200	Weak transcription	HSMM	muscle
30	chr7:39994400-39998000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:39994400-40000600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:39994600-40000800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:39994600-40000800	Weak transcription	Thymus	Thymus
34	chr7:39994600-40009000	Weak transcription	HMEC	breast
35	chr7:39994800-39996200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:39994800-39996200	Weak transcription	Fetal Intestine Large	intestine
37	chr7:39994800-39997600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:39994800-39999200	Weak transcription	NHDF-Ad	bronchial
39	chr7:39994800-39999400	Weak transcription	Colonic Mucosa	Colon
40	chr7:39994800-40000800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:39994800-40006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr7:39994800-40008000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:39994800-40008000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr7:39994800-40008400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:39994800-40008400	Weak transcription	NHEK	skin
46	chr7:39994800-40018000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr7:39995000-39996200	Weak transcription	Aorta	Aorta
48	chr7:39995000-39996600	Weak transcription	Fetal Kidney	kidney
49	chr7:39995000-39996600	Weak transcription	A549	lung
50	chr7:39995000-39996800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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