Variant report

Variant	rs2306097
Chromosome Location	chr9:100110179-100110180
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100109341..100111757-chr9:100115390..100116945,2	MCF-7	breast:
2	chr9:100108364..100110444-chr9:100117430..100119341,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197816	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10122063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1020884	0.91[EUR][1000 genomes]
rs1020885	0.91[EUR][1000 genomes]
rs1037948	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1037950	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1037951	0.90[EUR][1000 genomes]
rs10435867	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10435868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10448274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759527	0.88[CEU][hapmap]
rs10759624	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759657	0.91[EUR][1000 genomes]
rs10817273	0.89[CEU][hapmap]
rs10817286	0.89[CEU][hapmap]
rs10817487	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981280	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10981288	1.00[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10981296	1.00[YRI][hapmap]
rs10981329	1.00[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs10981438	0.85[ASN][1000 genomes]
rs10981890	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10981919	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs10981931	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11581	0.86[JPT][hapmap]
rs11791310	1.00[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12235305	0.85[ASN][1000 genomes]
rs13298346	1.00[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs13299627	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1542506	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1544203	1.00[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs1903635	0.81[JPT][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1947717	0.86[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2169456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2219664	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2242187	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279114	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493442	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2493443	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2502644	0.80[CHB][hapmap];0.88[JPT][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2615143	1.00[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2615145	1.00[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2795365	0.84[ASN][1000 genomes]
rs2795367	0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2818238	1.00[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2818239	0.83[ASN][1000 genomes]
rs2818243	0.93[ASW][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs3214072	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34955252	0.84[ASN][1000 genomes]
rs35609998	0.84[ASN][1000 genomes]
rs3747489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3747493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747496	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802471	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4313271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4366181	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4523384	0.84[ASN][1000 genomes]
rs4523385	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4554595	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742685	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742689	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4742690	0.91[EUR][1000 genomes]
rs4743072	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4743076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743077	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743087	0.96[CEU][hapmap]
rs4743088	0.96[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6478095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478131	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7020393	0.91[JPT][hapmap]
rs7042707	0.91[JPT][hapmap]
rs713066	1.00[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7470446	0.82[ASN][1000 genomes]
rs750674	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7856924	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7869536	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9696167	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	esv2761547	chr9:100109870-100115159	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2306097	RP11-498P14.5	cis	lung	GTEx
rs2306097	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs2306097	XPA	cis	parietal	SCAN
rs2306097	VN1R51P	cis	Thyroid	GTEx
rs2306097	RP11-520B13.4	cis	Thyroid	GTEx
rs2306097	TMOD1	cis	cerebellum	SCAN
rs2306097	ANKRD18CP	cis	Thyroid	GTEx
rs2306097	ECM2	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100070000-100131400	Weak transcription	Fetal Kidney	kidney
2	chr9:100077000-100140800	Weak transcription	Fetal Brain Male	brain
3	chr9:100080400-100126400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:100083800-100124000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:100086400-100110400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr9:100086600-100121600	Weak transcription	Right Ventricle	heart
7	chr9:100086600-100132000	Weak transcription	Thymus	Thymus
8	chr9:100088000-100126200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:100088200-100127000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr9:100088600-100128600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:100088600-100132800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:100088800-100121400	Weak transcription	Gastric	stomach
13	chr9:100089200-100128200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr9:100090600-100119000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:100090600-100133800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:100091600-100149200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr9:100093000-100111000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:100093000-100117000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr9:100093600-100122400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:100095600-100116800	Weak transcription	Brain Hippocampus Middle	brain
21	chr9:100099000-100132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:100104400-100117000	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:100104400-100118800	Weak transcription	Spleen	Spleen
24	chr9:100104400-100142000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:100104600-100110400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:100104600-100111000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:100104600-100118200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:100104600-100128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:100104800-100116800	Weak transcription	Fetal Intestine Large	intestine
30	chr9:100105000-100111600	Weak transcription	Fetal Intestine Small	intestine
31	chr9:100105200-100111000	Weak transcription	Lung	lung
32	chr9:100105200-100120800	Weak transcription	Psoas Muscle	Psoas
33	chr9:100105400-100127600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr9:100105800-100128000	Weak transcription	Brain Substantia Nigra	brain
35	chr9:100106400-100110200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr9:100106400-100118000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:100106800-100117200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr9:100106800-100128000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:100106800-100143200	Weak transcription	Liver	Liver
40	chr9:100107000-100117000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr9:100107000-100131400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr9:100107200-100112000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:100107200-100115600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr9:100107200-100117000	Weak transcription	Left Ventricle	heart
45	chr9:100107200-100130200	Weak transcription	Fetal Lung	lung
46	chr9:100107200-100138400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:100107800-100117200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:100108000-100148200	Weak transcription	Esophagus	oesophagus
49	chr9:100108800-100110800	Weak transcription	Fetal Brain Female	brain
50	chr9:100108800-100113400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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