Variant report

Variant	rs10247178
Chromosome Location	chr7:128193481-128193482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 34 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1003241	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10225988	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10237880	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10954193	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1109552	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11769769	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs11978608	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11982561	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12386751	0.87[ASN][1000 genomes]
rs12670271	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12670823	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12674125	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1450874	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs17169024	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs17169357	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2290229	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs28505422	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4077398	0.82[ASN][1000 genomes]
rs4554406	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4728128	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4728130	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4731479	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4731480	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4731484	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4731494	0.81[EUR][1000 genomes]
rs4731503	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs56033435	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56060467	0.80[ASN][1000 genomes]
rs58961149	0.83[ASN][1000 genomes]
rs60804557	0.82[ASN][1000 genomes]
rs62483297	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6467202	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6467203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6467210	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6955960	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6958788	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6969554	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs6975194	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6978360	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6979304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6979575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7385676	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7793136	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7793351	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7795558	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7797359	0.82[EUR][1000 genomes]
rs7797745	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7802233	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7804825	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7807293	0.82[AMR][1000 genomes];0.87[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	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

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs10247178	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs10247178	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs10247178	RP11-274B21.4	cis	Thyroid	GTEx
rs10247178	RP11-274B21.4	cis	Muscle Skeletal	GTEx
rs10247178	RP11-274B21.3	cis	Adipose Subcutaneous	GTEx
rs10247178	RP11-274B21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10247178	RP11-274B21.2	cis	Stomach	GTEx
rs10247178	RP11-274B21.4	cis	Stomach	GTEx
rs10247178	RP11-274B21.1	cis	lung	GTEx
rs10247178	RP11-274B21.4	cis	lung	GTEx
rs10247178	RP11-274B21.3	cis	Thyroid	GTEx
rs10247178	RP11-274B21.1	cis	Nerve Tibial	GTEx
rs10247178	RP11-274B21.2	cis	Muscle Skeletal	GTEx
rs10247178	RP11-274B21.4	cis	Whole Blood	GTEx
rs10247178	RP11-274B21.4	cis	Artery Tibial	GTEx
rs10247178	RP11-274B21.3	cis	Stomach	GTEx
rs10247178	RP11-274B21.2	cis	Nerve Tibial	GTEx
rs10247178	RP11-274B21.2	cis	Thyroid	GTEx
rs10247178	RP11-274B21.4	cis	Esophagus Muscularis	GTEx
rs10247178	RP11-274B21.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10247178	RP11-274B21.3	cis	Muscle Skeletal	GTEx
rs10247178	CICP14	cis	Adipose Subcutaneous	GTEx
rs10247178	CICP14	cis	lung	GTEx
rs10247178	RP11-274B21.2	cis	lung	GTEx
rs10247178	RP11-274B21.4	cis	Skin Sun Exposed Lower leg	GTEx
rs10247178	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs10247178	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs10247178	CICP14	cis	Artery Tibial	GTEx
rs10247178	RP11-274B21.4	cis	Esophagus Mucosa	GTEx
rs10247178	CICP14	cis	Thyroid	GTEx
rs10247178	RP11-274B21.1	cis	Whole Blood	GTEx
rs10247178	CICP14	cis	Esophagus Muscularis	GTEx
rs10247178	RP11-274B21.1	cis	Muscle Skeletal	GTEx
rs10247178	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128172600-128210800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:128172600-128214800	Weak transcription	Gastric	stomach
3	chr7:128172800-128239800	Weak transcription	Small Intestine	intestine
4	chr7:128173000-128231800	Weak transcription	Colonic Mucosa	Colon
5	chr7:128173000-128231800	Weak transcription	Fetal Kidney	kidney
6	chr7:128173600-128201000	Weak transcription	Psoas Muscle	Psoas
7	chr7:128173600-128214800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:128173800-128197800	Weak transcription	Right Atrium	heart
9	chr7:128173800-128199800	Weak transcription	Right Ventricle	heart
10	chr7:128173800-128201000	Weak transcription	Brain Germinal Matrix	brain
11	chr7:128173800-128214800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:128173800-128234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:128174000-128210600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:128174000-128220600	Weak transcription	NHLF	lung
15	chr7:128174000-128231800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:128174000-128232600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:128174600-128193600	Strong transcription	Fetal Stomach	stomach
18	chr7:128175400-128231800	Weak transcription	Left Ventricle	heart
19	chr7:128175800-128193600	Strong transcription	Fetal Intestine Small	intestine
20	chr7:128176000-128214800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:128177600-128231800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr7:128179200-128231800	Weak transcription	Esophagus	oesophagus
23	chr7:128181800-128231800	Weak transcription	Aorta	Aorta
24	chr7:128183000-128201000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:128183000-128214200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:128183400-128214800	Weak transcription	HUVEC	blood vessel
27	chr7:128183600-128196200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:128183600-128214800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr7:128185000-128210600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:128185200-128210000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:128185600-128194800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr7:128187400-128212400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr7:128187400-128214800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:128187400-128214800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:128187600-128196200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr7:128187600-128199000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:128187600-128200200	Weak transcription	A549	lung
38	chr7:128187600-128205200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr7:128187600-128213800	Weak transcription	Osteobl	bone
40	chr7:128187600-128214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:128187600-128232000	Weak transcription	NH-A	brain
42	chr7:128187800-128214800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr7:128188000-128199000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr7:128188000-128200400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr7:128188000-128208800	Weak transcription	K562	blood
46	chr7:128188000-128210800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:128188000-128213800	Weak transcription	Brain Anterior Caudate	brain
48	chr7:128188000-128213800	Weak transcription	Brain Hippocampus Middle	brain
49	chr7:128188000-128214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:128188000-128214800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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