Variant report

Variant	rs10876130
Chromosome Location	chr12:51452875-51452876
allele	A/G
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:1)
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	chr12:51440583..51444061-chr12:51452088..51456388,5	K562	blood:
2	chr12:51445938..51449687-chr12:51452701..51455734,3	MCF-7	breast:
3	chr12:51451364..51452891-chr12:51454083..51456493,2	K562	blood:
4	chr12:51439067..51445190-chr12:51449547..51456560,11	K562	blood:
5	chr12:51450731..51453622-chr12:51457605..51459306,2	K562	blood:
6	chr12:51452088..51454100-chr12:51476777..51478572,2	MCF-7	breast:
7	chr12:51440743..51444863-chr12:51448295..51453075,7	MCF-7	breast:
8	chr12:51452656..51454940-chr12:51460436..51462991,3	MCF-7	breast:
9	chr12:51444211..51450639-chr12:51451105..51456750,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIGD1C-1	chr12:51451254-51454201	NONHSAT028234

No data

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000050426	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10275	0.97[EUR][1000 genomes]
rs10783409	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs10876127	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876128	0.96[CEU][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs10876129	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876131	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10876132	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10876136	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10876138	0.85[CHB][hapmap]
rs10876139	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1095999	0.84[EUR][1000 genomes]
rs11169657	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11169695	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11169707	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169710	0.85[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11610644	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12370120	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12379	0.85[CHB][hapmap]
rs12424509	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12427345	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1486014	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs15756	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1632791	0.92[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17125111	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2029145	0.95[CEU][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2029146	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs224448	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs224572	0.88[CEU][hapmap];0.85[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs224575	0.81[CEU][hapmap]
rs2630371	0.80[EUR][1000 genomes]
rs319936	0.81[CEU][hapmap]
rs319939	0.81[CEU][hapmap]
rs370462	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3759405	0.85[CHB][hapmap]
rs427020	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4438107	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55874804	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61934800	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580782	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580785	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6580788	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs6580791	0.82[CHB][hapmap]
rs706805	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7135399	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7136960	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953867	0.85[CHB][hapmap]
rs7958068	0.90[EUR][1000 genomes]
rs7961626	0.85[EUR][1000 genomes]
rs7969803	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7971308	0.85[CHB][hapmap]
rs7976431	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7977740	0.85[EUR][1000 genomes]
rs829025	0.84[EUR][1000 genomes]
rs9739342	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10876130	DDN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:51443000-51453200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:51443600-51457400	Weak transcription	Fetal Brain Male	brain
5	chr12:51443600-51459600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:51443600-51462800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:51443800-51455600	Weak transcription	Fetal Heart	heart
8	chr12:51443800-51462600	Strong transcription	A549	lung
9	chr12:51444200-51454800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:51444200-51463200	Strong transcription	Placenta	Placenta
11	chr12:51444200-51465000	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:51444200-51465400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:51444200-51465600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:51444200-51470400	Strong transcription	Fetal Stomach	stomach
15	chr12:51444400-51462800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:51444400-51464800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr12:51444600-51455600	Strong transcription	Fetal Intestine Small	intestine
18	chr12:51445000-51467800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:51445400-51454000	Strong transcription	Left Ventricle	heart
20	chr12:51445400-51462600	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr12:51445400-51462600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:51445400-51462600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:51445400-51462800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:51445400-51464000	Strong transcription	Fetal Intestine Large	intestine
25	chr12:51445400-51467800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:51445400-51467800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr12:51445400-51469200	Strong transcription	Fetal Thymus	thymus
28	chr12:51445400-51470600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:51445600-51454200	Strong transcription	Thymus	Thymus
30	chr12:51445600-51456000	Strong transcription	Liver	Liver
31	chr12:51445600-51462400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:51445600-51462800	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr12:51445600-51462800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:51445600-51462800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:51445600-51462800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:51445600-51462800	Strong transcription	Primary T cells from cord blood	blood
37	chr12:51445600-51463000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:51445600-51463000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:51445600-51463800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:51445600-51465200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:51445600-51467400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr12:51445600-51467800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:51445600-51467800	Strong transcription	Adipose Nuclei	Adipose
44	chr12:51445600-51468000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr12:51445600-51468400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:51445600-51469200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:51445600-51469800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:51445600-51470400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:51445600-51470600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:51445800-51454200	Strong transcription	Brain Hippocampus Middle	brain

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