Variant report

Variant	rs10108
Chromosome Location	chr1:114516330-114516331
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114515162..114517888-chr1:114963803..114965626,2	MCF-7	breast:
2	chr1:114470804..114474068-chr1:114515316..114519565,7	MCF-7	breast:
3	chr1:114336878..114338564-chr1:114515485..114517158,2	K562	blood:
4	chr1:114513174..114515593-chr1:114515945..114517485,2	K562	blood:
5	chr1:114515711..114517385-chr1:114528473..114530458,2	MCF-7	breast:
6	chr1:114515271..114518013-chr1:115249909..115251463,2	K562	blood:
7	chr1:114446380..114448942-chr1:114514052..114516701,2	MCF-7	breast:
8	chr1:114495459..114498219-chr1:114516262..114517901,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235527	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10494162	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs10494163	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102703	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs11102706	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11102707	1.00[ASW][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11102708	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102709	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12127377	0.85[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12129050	0.85[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1217444	0.82[ASN][1000 genomes]
rs1503832	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1553449	0.87[ASN][1000 genomes]
rs1553450	0.85[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17852555	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1910485	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1985435	0.86[ASN][1000 genomes]
rs1985436	0.87[ASN][1000 genomes]
rs41302825	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6537800	0.81[ASN][1000 genomes]
rs6669370	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6674384	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs7364	0.94[CHB][hapmap];0.92[CHD][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs74111914	0.84[AFR][1000 genomes]
rs7519860	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7545300	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7546851	0.94[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs878129	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.82[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10108	PTPN22	cis	parietal	SCAN
rs10108	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs10108	DENND2C	cis	cerebellum	SCAN
rs10108	DCLRE1B	cis	uninvolved skin	skin_eQTL
rs10108	DCLRE1B	cis	lymphoblastoid	seeQTL
rs10108	DCLRE1B	cis	multi-tissue	Pritchard
rs10108	DCLRE1B	cis	normal skin	skin_eQTL
rs10108	DCLRE1B	cis	lesional skin	skin_eQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114479000-114517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114492800-114518600	Strong transcription	Dnd41	blood
3	chr1:114493400-114517600	Strong transcription	Fetal Thymus	thymus
4	chr1:114495400-114517400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:114495800-114516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:114495800-114518200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr1:114496000-114517000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:114496400-114516400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr1:114496400-114517000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:114496400-114517200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:114496400-114517400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:114496400-114517600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr1:114496400-114518200	Strong transcription	K562	blood
14	chr1:114496400-114519400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:114496600-114518800	Strong transcription	Primary B cells from cord blood	blood
16	chr1:114497000-114516400	Strong transcription	Fetal Intestine Large	intestine
17	chr1:114497000-114517000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:114497200-114516400	Strong transcription	Primary hematopoietic stem cells	blood
19	chr1:114497200-114516400	Strong transcription	GM12878-XiMat	blood
20	chr1:114497600-114517600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:114497800-114517400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:114498000-114517400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:114498800-114518200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:114500000-114517600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:114501800-114516800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:114503800-114517400	Strong transcription	Placenta	Placenta
27	chr1:114503800-114518600	Strong transcription	Brain Germinal Matrix	brain
28	chr1:114504200-114516800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:114504400-114517000	Strong transcription	Osteobl	bone
30	chr1:114504600-114517600	Strong transcription	HSMM	muscle
31	chr1:114504600-114517800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:114504600-114519000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:114504800-114516400	Strong transcription	Fetal Lung	lung
34	chr1:114504800-114516400	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:114504800-114516400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:114504800-114516600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr1:114504800-114517400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:114504800-114517600	Strong transcription	Primary T cells from cord blood	blood
39	chr1:114504800-114517600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:114504800-114517600	Strong transcription	NHDF-Ad	bronchial
41	chr1:114504800-114517800	Strong transcription	Liver	Liver
42	chr1:114504800-114518400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:114504800-114519400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:114505000-114516400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:114506000-114517800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:114506600-114517800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:114507000-114517200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:114507400-114516400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:114507600-114517000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:114507600-114517400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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