Variant report

Variant	rs10953541
Chromosome Location	chr7:107244545-107244546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107235719..107242565-chr7:107244340..107248517,9	K562	blood:
2	chr7:107219444..107222929-chr7:107242777..107244829,3	MCF-7	breast:
3	chr7:107220649..107224781-chr7:107243854..107248319,6	K562	blood:
4	chr7:107237613..107240026-chr7:107244497..107246419,2	K562	blood:

Variant related genes	Relation type
ENSG00000075790	Chromatin interaction
ENSG00000272854	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10464499	0.87[AFR][1000 genomes]
rs10464620	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10953540	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11532774	1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs12533694	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs12535761	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs12705420	1.00[ASW][hapmap]
rs13234124	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17403088	0.87[CHB][hapmap];0.87[AFR][1000 genomes]
rs17404067	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs17481621	0.87[AFR][1000 genomes]
rs17481842	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17482494	0.87[AFR][1000 genomes]
rs17486	0.87[AFR][1000 genomes]
rs2283041	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34273277	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34523267	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35024078	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35061190	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35531458	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730248	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4730250	0.94[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs56949084	0.87[AFR][1000 genomes]
rs68170813	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6943051	1.00[MKK][hapmap]
rs6955488	0.87[AFR][1000 genomes]
rs6957186	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs6958969	0.87[AFR][1000 genomes]
rs6964395	0.87[AFR][1000 genomes]
rs763386	0.94[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes]
rs7784906	0.87[AFR][1000 genomes]
rs7785962	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797791	0.87[AFR][1000 genomes]
rs8180747	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv482365	chr7:107122401-107271861	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv608074	chr7:107179131-107260856	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary heart disease	21378988	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10953541	HBP1	cis	cerebellum	SCAN
rs10953541	GPR22	Cis_1M	lymphoblastoid	RTeQTL
rs10953541	COG5	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107221200-107272000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:107221400-107253800	Weak transcription	Ovary	ovary
3	chr7:107221400-107254200	Weak transcription	Thymus	Thymus
4	chr7:107221400-107256400	Weak transcription	Lung	lung
5	chr7:107221400-107272400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:107221400-107276000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:107221600-107254200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:107221800-107249400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:107222400-107258200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr7:107223000-107254400	Weak transcription	Brain Germinal Matrix	brain
11	chr7:107223400-107256800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr7:107223600-107254400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:107223600-107256600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:107225600-107254000	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:107226200-107254000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:107226800-107254200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:107226800-107254800	Weak transcription	Fetal Thymus	thymus
18	chr7:107227800-107253800	Weak transcription	Brain Angular Gyrus	brain
19	chr7:107227800-107265400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:107229400-107245800	Weak transcription	Right Ventricle	heart
21	chr7:107229600-107249600	Weak transcription	Brain Anterior Caudate	brain
22	chr7:107230200-107256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:107233600-107256800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:107234200-107246200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:107234400-107244800	Strong transcription	Placenta	Placenta
26	chr7:107235200-107271800	Weak transcription	Small Intestine	intestine
27	chr7:107235800-107245800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:107235800-107247400	Weak transcription	Fetal Stomach	stomach
29	chr7:107235800-107249400	Weak transcription	Aorta	Aorta
30	chr7:107235800-107254000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:107235800-107254400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:107235800-107268200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:107236000-107245400	Weak transcription	Fetal Brain Female	brain
34	chr7:107236000-107245800	Weak transcription	Fetal Brain Male	brain
35	chr7:107236000-107249200	Weak transcription	Fetal Lung	lung
36	chr7:107236000-107249400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:107236000-107249800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr7:107236000-107254400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:107236000-107254600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:107236000-107262800	Weak transcription	GM12878-XiMat	blood
41	chr7:107236000-107270800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:107236200-107247000	Weak transcription	Fetal Intestine Large	intestine
43	chr7:107236200-107249400	Weak transcription	Fetal Kidney	kidney
44	chr7:107236400-107255000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr7:107236400-107256600	Weak transcription	A549	lung
46	chr7:107236600-107254000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr7:107236800-107249200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:107237200-107254400	Weak transcription	NHLF	lung
49	chr7:107237600-107247000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr7:107237600-107250400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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