Variant report

Variant	rs2169456
Chromosome Location	chr9:100132194-100132195
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDRD7-1	chr9:100131560-100132364	NONHSAT133501

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10122063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10125198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10435868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10448274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10759527	0.85[CEU][hapmap]
rs10817273	0.86[CEU][hapmap]
rs10817286	0.86[CEU][hapmap]
rs10981280	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10981288	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10981329	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10981890	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10981919	0.96[CEU][hapmap]
rs10981931	0.96[CEU][hapmap]
rs11581	0.86[JPT][hapmap]
rs11791310	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13298346	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13299627	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1542506	0.96[CEU][hapmap]
rs1544203	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1903635	0.81[JPT][hapmap]
rs1947717	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2219664	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2242187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2306097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2493442	0.81[CHB][hapmap]
rs2502644	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2615143	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2615145	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2795367	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2818238	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2818243	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs3214072	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3747489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3747493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3747496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4237189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4313271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4366181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4523385	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs4742689	0.96[CEU][hapmap]
rs4743072	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4743076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4743077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4743084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4743087	0.96[CEU][hapmap]
rs4743088	0.96[CEU][hapmap]
rs6478095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7020393	0.91[JPT][hapmap]
rs7042707	0.91[JPT][hapmap]
rs713066	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs750674	0.95[CHB][hapmap];0.95[JPT][hapmap]

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	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2169456	RP11-520B13.4	cis	Thyroid	GTEx
rs2169456	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs2169456	ANKRD18CP	cis	Thyroid	GTEx
rs2169456	LOC340508	cis	brain	BrainEAC
rs2169456	VN1R51P	cis	Thyroid	GTEx
rs2169456	RP11-498P14.5	cis	lung	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100077000-100140800	Weak transcription	Fetal Brain Male	brain
2	chr9:100088600-100132800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr9:100090600-100133800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr9:100091600-100149200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr9:100099000-100132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:100104400-100142000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:100106800-100143200	Weak transcription	Liver	Liver
8	chr9:100107200-100138400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:100108000-100148200	Weak transcription	Esophagus	oesophagus
10	chr9:100110200-100132200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr9:100115400-100144600	Weak transcription	Hela-S3	cervix
12	chr9:100115600-100139200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:100117400-100132400	Weak transcription	Fetal Intestine Large	intestine
14	chr9:100117400-100145000	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:100117600-100146400	Weak transcription	Small Intestine	intestine
16	chr9:100118200-100132400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:100118200-100141600	Weak transcription	Primary T cells from cord blood	blood
18	chr9:100120000-100137800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr9:100121800-100137800	Weak transcription	Gastric	stomach
20	chr9:100125400-100132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:100126400-100137800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr9:100126600-100141600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr9:100126600-100148400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:100127000-100148600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:100128800-100132600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:100129000-100132200	Weak transcription	Lung	lung
27	chr9:100129000-100132400	Weak transcription	Brain Angular Gyrus	brain
28	chr9:100129000-100132400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:100129000-100134800	Weak transcription	Spleen	Spleen
30	chr9:100129000-100137200	Weak transcription	Aorta	Aorta
31	chr9:100129000-100137800	Weak transcription	Pancreas	Pancrea
32	chr9:100129000-100138200	Weak transcription	Brain Substantia Nigra	brain
33	chr9:100129000-100144400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:100129200-100132200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr9:100129200-100132400	Weak transcription	Right Ventricle	heart
36	chr9:100129200-100132400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr9:100129200-100132600	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:100129200-100137200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:100129200-100137600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:100129600-100138600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:100130000-100133200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:100130200-100132600	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr9:100130600-100132800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:100130800-100132200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
45	chr9:100131000-100132600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:100131400-100132200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:100131400-100132600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr9:100131400-100132600	ZNF genes & repeats	Fetal Lung	lung
49	chr9:100131400-100132800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
50	chr9:100131400-100133000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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