Variant report

Variant	rs10259359
Chromosome Location	chr7:128233201-128233202
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10085435	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224862	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10227608	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233059	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241185	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs10250369	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253131	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10261037	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269844	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270431	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10270985	0.81[EUR][1000 genomes]
rs10954205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11760285	1.00[ASN][1000 genomes]
rs11761312	0.85[AMR][1000 genomes]
rs11761662	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11766319	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11769546	1.00[ASN][1000 genomes]
rs11770604	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11771884	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333625	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12530672	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12535238	0.80[EUR][1000 genomes]
rs12537208	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224451	0.82[AFR][1000 genomes]
rs13224613	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13224784	0.85[AFR][1000 genomes]
rs13226592	0.83[AFR][1000 genomes]
rs13233377	0.80[EUR][1000 genomes]
rs13235219	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13246302	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247746	0.87[AFR][1000 genomes]
rs28496126	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521260	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521711	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs339070	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs339079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs339093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs34120723	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34125589	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34490491	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34751214	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34887739	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35247963	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35825132	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35871589	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3816421	0.86[EUR][1000 genomes]
rs4289745	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4338038	0.82[AFR][1000 genomes]
rs55953818	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57049631	0.92[AFR][1000 genomes]
rs60029447	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467184	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467201	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6943737	0.80[EUR][1000 genomes]
rs6946179	0.80[EUR][1000 genomes]
rs6958343	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960296	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6961754	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6963982	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967393	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6969343	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971819	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6972787	0.80[EUR][1000 genomes]
rs6976879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6977126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71546785	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71546786	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71548762	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71578280	1.00[ASN][1000 genomes]
rs7776915	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777625	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7778169	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7778731	0.82[AMR][1000 genomes]
rs7786772	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787764	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7790478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7794447	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7798172	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801678	0.81[AFR][1000 genomes]
rs7804472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7810047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7811083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9690225	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690934	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9692416	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9768808	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9769753	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1848097	chr7:128179503-128248497	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
3	esv1810084	chr7:128201902-128248697	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1829966	chr7:128201902-128248697	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1847512	chr7:128201902-128248697	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv966885	chr7:128212815-128256300	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10259359	CICP14	cis	Nerve Tibial	GTEx
rs10259359	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs10259359	RP11-274B21.10	cis	Nerve Tibial	GTEx
rs10259359	RP11-274B21.10	cis	Thyroid	GTEx
rs10259359	CICP14	cis	Muscle Skeletal	GTEx
rs10259359	CICP14	cis	Thyroid	GTEx
rs10259359	RP11-274B21.10	cis	Skin Sun Exposed Lower leg	GTEx
rs10259359	CICP14	cis	lung	GTEx
rs10259359	RP11-274B21.10	cis	Esophagus Muscularis	GTEx
rs10259359	RP11-274B21.10	cis	Esophagus Mucosa	GTEx
rs10259359	CICP14	cis	Artery Tibial	GTEx
rs10259359	CICP14	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128172800-128239800	Weak transcription	Small Intestine	intestine
2	chr7:128173800-128234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:128197800-128241800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:128200000-128258800	Weak transcription	Right Ventricle	heart
5	chr7:128204800-128258800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:128213400-128238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:128217800-128244000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr7:128219400-128249200	Weak transcription	Fetal Heart	heart
9	chr7:128220800-128249200	Weak transcription	A549	lung
10	chr7:128221000-128236400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:128223800-128258800	Weak transcription	Lung	lung
12	chr7:128226400-128258800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:128229400-128237200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr7:128229800-128234400	Strong transcription	HSMM	muscle
15	chr7:128229800-128235000	Strong transcription	Dnd41	blood
16	chr7:128229800-128235800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:128230000-128249200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr7:128230400-128237600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:128230600-128234800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:128230800-128233400	Strong transcription	Fetal Intestine Small	intestine
21	chr7:128230800-128234600	Strong transcription	Primary T cells from cord blood	blood
22	chr7:128230800-128234800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:128230800-128237600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:128230800-128240400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:128231000-128237200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:128231000-128241800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:128231200-128233400	Strong transcription	Pancreas	Pancrea
28	chr7:128231200-128236000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:128231600-128233600	Strong transcription	GM12878-XiMat	blood
30	chr7:128231600-128233800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr7:128231600-128234400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:128231600-128234400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr7:128231600-128235400	Strong transcription	Osteobl	bone
34	chr7:128231600-128235600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:128231600-128235800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr7:128231600-128237200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:128231800-128233400	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr7:128231800-128233400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr7:128231800-128233400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:128231800-128233400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:128231800-128233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr7:128231800-128233400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr7:128231800-128233400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:128231800-128233400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:128231800-128233400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:128231800-128233400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:128231800-128233400	Genic enhancers	Brain Angular Gyrus	brain
48	chr7:128231800-128233400	Genic enhancers	Brain Hippocampus Middle	brain
49	chr7:128231800-128233400	Genic enhancers	Brain Inferior Temporal Lobe	brain
50	chr7:128231800-128233400	Strong transcription	Colonic Mucosa	Colon

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