Variant report

Variant	rs10954205
Chromosome Location	chr7:128307573-128307574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:128306825..128310882-chr7:128311566..128316462,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71F2-5	chr7:128307097-128308210	ENSG00000271553.1

Variant related genes	Relation type
ENSG00000205085	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10085435	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10224862	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10227608	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10233059	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10241185	0.89[EUR][1000 genomes]
rs10242806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10250369	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10253131	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10259359	0.87[EUR][1000 genomes]
rs10261037	0.82[AFR][1000 genomes]
rs10269844	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10270431	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10270985	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10274878	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10276810	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11761312	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11766319	0.80[EUR][1000 genomes]
rs11768485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771884	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12333625	0.91[EUR][1000 genomes]
rs12530672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs12535238	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12536288	1.00[ASN][1000 genomes]
rs12537208	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12706858	0.89[ASN][1000 genomes]
rs13224613	0.91[EUR][1000 genomes]
rs13233377	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13235219	0.91[EUR][1000 genomes]
rs13237593	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13246302	0.84[EUR][1000 genomes]
rs28496126	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28521260	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28521711	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs339070	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs339071	0.89[ASN][1000 genomes]
rs339074	0.89[ASN][1000 genomes]
rs339079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs339093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34120723	0.89[EUR][1000 genomes]
rs34125589	0.83[AMR][1000 genomes]
rs34490491	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34751214	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34757247	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34942906	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34960471	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35247963	0.93[EUR][1000 genomes]
rs35603038	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs35825132	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35871589	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816421	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4289745	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55953818	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60029447	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6467181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6467184	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6467201	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6467205	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6943737	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6946179	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6958343	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6960296	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961754	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6963982	0.82[EUR][1000 genomes]
rs6967393	0.91[EUR][1000 genomes]
rs6969343	0.82[EUR][1000 genomes]
rs6971819	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6972787	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6976879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6977126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71546785	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71546786	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71546790	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs71548762	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7776915	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7777625	0.84[EUR][1000 genomes]
rs7778169	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7778731	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7786772	0.82[EUR][1000 genomes]
rs7787764	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790478	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs7794447	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7798172	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7804472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7810047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7811083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690225	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9690934	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9692416	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9768808	0.93[EUR][1000 genomes]
rs9769753	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10954205	CICP14	cis	Thyroid	GTEx
rs10954205	RP11-274B21.10	cis	Esophagus Muscularis	GTEx
rs10954205	RP11-274B21.10	cis	Thyroid	GTEx
rs10954205	CICP14	cis	lung	GTEx
rs10954205	METTL2B	cis	Artery Tibial	GTEx
rs10954205	METTL2B	cis	Skin Sun Exposed Lower leg	GTEx
rs10954205	CICP14	cis	Muscle Skeletal	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128249600-128308400	Weak transcription	HSMM	muscle
2	chr7:128249600-128312200	Weak transcription	Psoas Muscle	Psoas
3	chr7:128249600-128319600	Weak transcription	NHLF	lung
4	chr7:128282400-128312400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr7:128284200-128313200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:128284400-128313200	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:128293600-128312200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr7:128294000-128313200	Weak transcription	Brain Germinal Matrix	brain
9	chr7:128294800-128328000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:128295000-128310400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:128295000-128311000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:128295000-128319800	Weak transcription	Left Ventricle	heart
13	chr7:128295000-128319800	Weak transcription	Right Ventricle	heart
14	chr7:128295000-128325200	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:128295400-128325400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:128298600-128329200	Weak transcription	Pancreas	Pancrea
17	chr7:128300200-128313200	Weak transcription	Right Atrium	heart
18	chr7:128301800-128310600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:128302000-128308400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:128302200-128318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:128302400-128312000	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:128302400-128319800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:128302400-128323200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:128302400-128323200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:128302400-128324000	Weak transcription	Aorta	Aorta
26	chr7:128302400-128337200	Weak transcription	Gastric	stomach
27	chr7:128302600-128310600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:128302600-128312800	Weak transcription	Fetal Stomach	stomach
29	chr7:128302600-128323000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr7:128302600-128327800	Weak transcription	Placenta	Placenta
31	chr7:128302800-128321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:128303000-128312800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr7:128303600-128319400	Weak transcription	Fetal Brain Female	brain
34	chr7:128305000-128323000	Weak transcription	NHDF-Ad	bronchial
35	chr7:128305400-128310400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:128305400-128317600	Weak transcription	Osteobl	bone
37	chr7:128305800-128309600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:128305800-128311800	Weak transcription	HUVEC	blood vessel
39	chr7:128307200-128313000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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