Variant report

Variant	rs17610836
Chromosome Location	chr6:35057479-35057480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1093986	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11552398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196771	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13203612	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206654	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207848	0.85[EUR][1000 genomes]
rs13208078	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13214114	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216424	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13219307	0.83[ASN][1000 genomes]
rs16871749	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16871809	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16871814	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896559	0.86[ASN][1000 genomes]
rs1747516	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1747517	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17611877	0.97[ASN][1000 genomes]
rs2177382	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2234044	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395608	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2494098	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2762336	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820225	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34069418	0.89[ASN][1000 genomes]
rs34103100	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34208177	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34250961	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34715060	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34930033	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35095464	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35693439	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756856	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41270050	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4628094	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57111149	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66579470	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66753029	0.84[EUR][1000 genomes]
rs67167177	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67638810	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67941146	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6899618	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906666	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913286	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913975	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926532	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936337	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942104	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728238	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896254	0.89[ASN][1000 genomes]
rs72897804	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72901705	0.98[ASN][1000 genomes]
rs7766770	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767073	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820061	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820062	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820063	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820065	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820066	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820067	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820069	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820072	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820083	0.86[ASN][1000 genomes]
rs820095	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs820099	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820100	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820101	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820103	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs843937	0.86[ASN][1000 genomes]
rs865352	0.81[AMR][1000 genomes]
rs9462053	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462054	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9469950	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv869750	chr6:35031548-35085585	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17610836	TCP11	cis	Skin Sun Exposed Lower leg	GTEx
rs17610836	TCP11	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35018800-35060600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:35020000-35059800	Strong transcription	Fetal Intestine Small	intestine
3	chr6:35020400-35059400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:35024800-35062000	Weak transcription	A549	lung
5	chr6:35026600-35059200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:35028600-35060000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:35036200-35059200	Strong transcription	Primary T cells from cord blood	blood
8	chr6:35037000-35061800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:35039400-35060600	Strong transcription	Fetal Intestine Large	intestine
10	chr6:35042200-35059200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:35044400-35058800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr6:35044600-35057600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr6:35044600-35058200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:35044800-35057800	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr6:35044800-35058800	Strong transcription	Gastric	stomach
16	chr6:35044800-35059000	Strong transcription	Left Ventricle	heart
17	chr6:35045000-35057800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:35045000-35059000	Strong transcription	Pancreas	Pancrea
19	chr6:35045200-35057800	Strong transcription	Brain Germinal Matrix	brain
20	chr6:35045200-35059400	Strong transcription	Thymus	Thymus
21	chr6:35046400-35057800	Strong transcription	Fetal Lung	lung
22	chr6:35049600-35058800	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr6:35049600-35060200	Weak transcription	Psoas Muscle	Psoas
24	chr6:35050000-35059800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr6:35050000-35063800	Weak transcription	HUVEC	blood vessel
26	chr6:35050200-35059600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr6:35050600-35057600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:35050600-35058800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:35050600-35060200	Weak transcription	Right Atrium	heart
30	chr6:35050800-35057600	Strong transcription	Colonic Mucosa	Colon
31	chr6:35051000-35058400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:35051400-35061400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:35051800-35064000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:35052000-35058200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:35052400-35058400	Strong transcription	Fetal Muscle Leg	muscle
36	chr6:35052400-35059200	Strong transcription	Brain Cingulate Gyrus	brain
37	chr6:35052800-35058000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr6:35052800-35058400	Strong transcription	Brain Substantia Nigra	brain
39	chr6:35052800-35060000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:35053400-35060200	Weak transcription	Fetal Kidney	kidney
41	chr6:35053400-35064200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:35053600-35058400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:35054000-35060000	Genic enhancers	Placenta	Placenta
44	chr6:35054000-35063800	Weak transcription	Stomach Mucosa	stomach
45	chr6:35054200-35057600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:35054200-35059200	Genic enhancers	Stomach Smooth Muscle	stomach
47	chr6:35054600-35058200	Genic enhancers	Right Ventricle	heart
48	chr6:35054600-35059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:35055000-35064000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:35055200-35059800	Genic enhancers	Adipose Nuclei	Adipose

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