Variant report

Variant	rs10956940
Chromosome Location	chr8:96172490-96172491
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:96161791..96169135-chr8:96169356..96174766,9	MCF-7	breast:
2	chr8:96170992..96173678-chr8:96173856..96175498,2	K562	blood:
3	chr8:96166402..96170248-chr8:96170840..96172689,3	MCF-7	breast:
4	chr8:96171498..96173321-chr8:96177174..96178804,2	K562	blood:
5	chr8:96170558..96173425-chr8:96180616..96182555,2	K562	blood:
6	chr8:96145309..96147503-chr8:96171057..96172593,2	MCF-7	breast:
7	chr8:96068974..96069736-chr8:96172085..96172944,4	MCF-7	breast:
8	chr8:96163910..96166560-chr8:96171762..96173400,2	K562	blood:
9	chr8:96079342..96079849-chr8:96171843..96172496,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175895	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10090946	1.00[ASN][1000 genomes]
rs10956937	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13249202	1.00[ASN][1000 genomes]
rs16917378	1.00[CHB][hapmap]
rs169863	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169864	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192714	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297555	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297559	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3174076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6998622	1.00[ASN][1000 genomes]
rs7839455	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv819397	chr8:96168255-96177678	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10956940	PGCP	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96150400-96179200	Weak transcription	Fetal Lung	lung
2	chr8:96162400-96178800	Weak transcription	NH-A	brain
3	chr8:96163200-96175400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:96164600-96174800	Weak transcription	HUVEC	blood vessel
5	chr8:96164800-96175000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr8:96165000-96174600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr8:96165200-96174400	Weak transcription	Dnd41	blood
8	chr8:96165600-96174600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr8:96165800-96175000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr8:96166000-96175000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr8:96166800-96173800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr8:96167000-96172600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:96167200-96174800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr8:96167200-96178600	Weak transcription	Right Ventricle	heart
15	chr8:96167200-96179200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr8:96167200-96179400	Weak transcription	Brain Angular Gyrus	brain
17	chr8:96167200-96179600	Weak transcription	Brain Anterior Caudate	brain
18	chr8:96167200-96179600	Weak transcription	Left Ventricle	heart
19	chr8:96167200-96181600	Weak transcription	Small Intestine	intestine
20	chr8:96167400-96174800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr8:96167400-96175000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr8:96167400-96179600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr8:96167600-96174400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr8:96167600-96180600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr8:96167600-96181400	Weak transcription	Liver	Liver
26	chr8:96169400-96181000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr8:96169600-96174200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr8:96169600-96176000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr8:96169800-96175800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr8:96169800-96175800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr8:96170000-96180200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr8:96170200-96179600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr8:96170200-96181000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr8:96171000-96172600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr8:96171000-96172600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
36	chr8:96171000-96175000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr8:96171200-96172600	Strong transcription	Primary T cells from cord blood	blood
38	chr8:96171200-96172600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr8:96171200-96172600	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr8:96171200-96172600	ZNF genes & repeats	Fetal Muscle Leg	muscle
41	chr8:96171400-96172600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr8:96171400-96172600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr8:96171400-96172600	ZNF genes & repeats	Fetal Thymus	thymus
44	chr8:96171600-96172600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr8:96171600-96172600	ZNF genes & repeats	Fetal Stomach	stomach
46	chr8:96171800-96172600	ZNF genes & repeats	Ovary	ovary
47	chr8:96171800-96179400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr8:96172000-96172600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr8:96172000-96172600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr8:96172000-96172600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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