Variant report

Variant	rs322823
Chromosome Location	chr7:127727400-127727401
allele	A/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	chr7:127723452-127728216	K562	blood:	n/a	n/a
2	POLR2A	chr7:127727324-127727529	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:127727179-127727741	K562	blood:	n/a	n/a
4	POLR2A	chr7:127727240-127727599	K562	blood:	n/a	n/a
5	POLR2A	chr7:127727220-127727509	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127724628..127729204-chr7:127729479..127734634,5	MCF-7	breast:

Variant related genes	Relation type
SND1	TF binding region
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1024910	0.85[AMR][1000 genomes]
rs1193333	0.82[AMR][1000 genomes]
rs1193335	0.83[AMR][1000 genomes]
rs124756	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1345509	0.83[JPT][hapmap]
rs2241291	0.85[CHB][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs2543477	0.81[AMR][1000 genomes]
rs322781	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs322813	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322816	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322817	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs322819	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322820	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322821	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322822	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs322824	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322825	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322826	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs322827	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs322828	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs322829	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322830	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322832	0.94[ASN][1000 genomes]
rs322833	0.94[ASN][1000 genomes]
rs322837	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322840	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757753	0.95[ASN][1000 genomes]
rs3757754	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757759	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3757760	0.85[CHB][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs3757763	0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs3779522	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3779523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779526	0.83[JPT][hapmap]
rs3779527	0.89[AMR][1000 genomes]
rs3808055	0.95[ASN][1000 genomes]
rs3808056	0.84[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap]
rs3823995	0.83[JPT][hapmap]
rs6467155	0.87[AMR][1000 genomes]
rs6467156	0.87[AMR][1000 genomes]
rs6969233	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6973092	0.83[JPT][hapmap]
rs7789322	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs322823	GCC1	cis	lymphoblastoid	seeQTL
rs322823	GPR37	cis	cerebellum	SCAN
rs322823	CCDC136	cis	parietal	SCAN

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127702800-127727800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:127707800-127742200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:127710600-127737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:127711600-127727400	Strong transcription	HepG2	liver
5	chr7:127711600-127735600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr7:127711600-127736400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:127711800-127737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:127712000-127728800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:127712200-127738200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr7:127713000-127735000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr7:127713000-127737200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:127713200-127729600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:127713200-127736400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:127713400-127736400	Strong transcription	NHEK	skin
15	chr7:127713800-127738800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:127714400-127735000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr7:127714400-127738000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr7:127714800-127734400	Strong transcription	Dnd41	blood
19	chr7:127715800-127738400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:127717000-127729000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr7:127717000-127738000	Weak transcription	Fetal Kidney	kidney
22	chr7:127717200-127734000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:127717200-127736600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:127717200-127738600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:127717600-127729600	Strong transcription	Lung	lung
26	chr7:127717600-127736600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:127717600-127738800	Strong transcription	Liver	Liver
28	chr7:127717800-127728800	Strong transcription	Fetal Intestine Large	intestine
29	chr7:127717800-127736600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:127718000-127728200	Strong transcription	Adipose Nuclei	Adipose
31	chr7:127718200-127728000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr7:127718200-127736400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr7:127718200-127736400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr7:127718400-127732800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:127718400-127736600	Strong transcription	Gastric	stomach
36	chr7:127718600-127727800	Weak transcription	Brain Germinal Matrix	brain
37	chr7:127719200-127736400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr7:127720000-127736000	Weak transcription	Psoas Muscle	Psoas
39	chr7:127720400-127733200	Strong transcription	Primary B cells from cord blood	blood
40	chr7:127720600-127738200	Strong transcription	GM12878-XiMat	blood
41	chr7:127721200-127733000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr7:127721200-127735800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:127721400-127733800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr7:127721400-127733800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:127721400-127734800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr7:127721400-127735000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:127722400-127738400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:127722600-127729600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:127722600-127730000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:127723200-127729600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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