Variant report

Variant	rs10953830
Chromosome Location	chr7:116534747-116534748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:116534294..116537444-chr7:116540535..116543196,3	K562	blood:
2	chr7:116530663..116533165-chr7:116534144..116536463,3	MCF-7	breast:
3	chr7:116522756..116525769-chr7:116533074..116536831,3	K562	blood:
4	7:115847372-115857098..7:116532782-116535085	GM12878	blood:

Variant related genes	Relation type
ENSG00000135269	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10487354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953831	0.80[TSI][hapmap]
rs12533164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665952	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12669383	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12670056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12671827	0.94[EUR][1000 genomes]
rs12671828	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12672008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673979	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12674017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12706108	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706109	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12706110	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706112	0.99[EUR][1000 genomes]
rs12706115	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706120	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12706121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706122	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706123	0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs13222845	0.94[EUR][1000 genomes]
rs13224082	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13228847	0.97[EUR][1000 genomes]
rs13239000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237720	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299441	0.95[EUR][1000 genomes]
rs2301649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3173936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807999	0.88[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs4808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804651	0.85[TSI][hapmap]
rs7808129	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9791492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv831107	chr7:116414734-116649466	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116503800-116554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:116504600-116540800	Weak transcription	Fetal Kidney	kidney
3	chr7:116505000-116537400	Weak transcription	Brain Germinal Matrix	brain
4	chr7:116506000-116554600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:116511400-116554600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:116512000-116545400	Weak transcription	NHLF	lung
7	chr7:116514600-116537800	Weak transcription	NHEK	skin
8	chr7:116515400-116559200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:116516800-116551200	Weak transcription	Brain Angular Gyrus	brain
10	chr7:116517200-116538000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:116517200-116554600	Weak transcription	Esophagus	oesophagus
12	chr7:116517600-116556600	Weak transcription	Psoas Muscle	Psoas
13	chr7:116520000-116551200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:116520200-116538000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:116520200-116541000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:116522800-116534800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:116524600-116542200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr7:116524600-116543800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:116525200-116535000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr7:116525200-116540600	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:116525400-116537000	Strong transcription	Fetal Thymus	thymus
22	chr7:116525800-116551200	Weak transcription	Thymus	Thymus
23	chr7:116525800-116554600	Weak transcription	Aorta	Aorta
24	chr7:116525800-116558400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr7:116525800-116559400	Weak transcription	Colonic Mucosa	Colon
26	chr7:116526000-116540600	Weak transcription	Fetal Brain Male	brain
27	chr7:116526000-116543800	Weak transcription	Lung	lung
28	chr7:116526200-116550000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr7:116526200-116551200	Weak transcription	Small Intestine	intestine
30	chr7:116526400-116541600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr7:116526600-116537800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr7:116526600-116540600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:116526600-116545400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:116526600-116553600	Weak transcription	Right Ventricle	heart
35	chr7:116526800-116535400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:116526800-116543200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:116526800-116546800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr7:116526800-116554600	Weak transcription	Gastric	stomach
39	chr7:116526800-116559400	Weak transcription	Stomach Mucosa	stomach
40	chr7:116527000-116539400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr7:116527000-116543800	Weak transcription	Ovary	ovary
42	chr7:116527000-116546200	Weak transcription	Brain Anterior Caudate	brain
43	chr7:116527000-116560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:116527200-116549600	Weak transcription	Fetal Heart	heart
45	chr7:116528000-116535000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr7:116528000-116535600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr7:116528000-116535600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr7:116528000-116536400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:116528000-116540800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr7:116528200-116535200	Strong transcription	Placenta	Placenta

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