Variant report

Variant	rs12171104
Chromosome Location	chr22:28317669-28317670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr22:28317650-28317910	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28317023..28318646-chr22:28319576..28321605,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-1	chr22:28317460-28318778	NONHSAT084626

Variant related genes	Relation type
PITPNB	TF binding region
MIR3199-2	TF binding region

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10154425	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10212036	0.81[EUR][1000 genomes]
rs10483140	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483142	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10483143	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs118840	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12165651	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165797	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166023	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12166077	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12166158	0.86[EUR][1000 genomes]
rs12166256	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12166389	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166719	0.80[AMR][1000 genomes]
rs12166740	0.89[EUR][1000 genomes]
rs12166912	0.86[EUR][1000 genomes]
rs12166938	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12167320	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167829	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168054	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs12168180	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12168251	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12168582	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169097	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12169888	0.91[EUR][1000 genomes]
rs12169936	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170022	0.86[EUR][1000 genomes]
rs12170558	0.80[AMR][1000 genomes]
rs12170953	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs138636	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs138637	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs138639	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs138640	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs138642	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs138646	0.81[CEU][hapmap]
rs138651	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs138653	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs138654	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs138655	0.91[EUR][1000 genomes]
rs138656	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs138658	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs138660	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs138664	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs138665	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs138667	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs138669	0.84[EUR][1000 genomes]
rs138670	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs138671	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs138672	0.91[EUR][1000 genomes]
rs16985763	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16985967	0.80[AMR][1000 genomes]
rs16986037	0.86[EUR][1000 genomes]
rs16986077	0.81[EUR][1000 genomes]
rs16987005	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17390800	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407024	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs17483887	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs17484337	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2745562	0.87[CEU][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28375646	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs470098	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs470101	0.90[CEU][hapmap]
rs470102	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs470103	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs470104	0.91[EUR][1000 genomes]
rs55856549	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56233401	0.86[EUR][1000 genomes]
rs56393679	0.80[AMR][1000 genomes]
rs57686964	0.86[EUR][1000 genomes]
rs58050941	0.86[EUR][1000 genomes]
rs58823697	0.86[EUR][1000 genomes]
rs7286519	0.91[EUR][1000 genomes]
rs7288331	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289984	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7292562	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73880355	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73880374	0.91[EUR][1000 genomes]
rs73880375	0.91[EUR][1000 genomes]
rs73880376	0.91[EUR][1000 genomes]
rs73880381	0.91[EUR][1000 genomes]
rs73880382	0.84[EUR][1000 genomes]
rs73880383	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73880384	0.81[EUR][1000 genomes]
rs73880387	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73880393	0.84[EUR][1000 genomes]
rs761323	0.86[EUR][1000 genomes]
rs8141163	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141173	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620752	0.81[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620753	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620755	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9620757	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620762	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs9620764	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs9620766	0.80[AMR][1000 genomes]
rs9620767	0.80[AMR][1000 genomes]
rs9620768	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9620769	0.84[EUR][1000 genomes]
rs9620771	0.84[EUR][1000 genomes]
rs9625361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625363	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625366	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625367	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625370	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625375	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625377	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625387	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs9625388	0.91[EUR][1000 genomes]
rs9625390	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs9625391	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs9625393	0.81[EUR][1000 genomes]
rs9625395	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625403	0.80[AMR][1000 genomes]
rs9625408	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs9625409	0.84[EUR][1000 genomes]
rs9625410	0.83[EUR][1000 genomes]
rs9625413	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625415	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9625416	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625417	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9625418	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9625421	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9985213	0.97[AMR][1000 genomes];0.98[EUR][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28316000-28317800	Enhancers	Small Intestine	intestine
2	chr22:28316200-28326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:28316200-28328400	Weak transcription	Aorta	Aorta
4	chr22:28316200-28337400	Weak transcription	Ovary	ovary
5	chr22:28316400-28317800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr22:28316400-28317800	Enhancers	Fetal Heart	heart
7	chr22:28316400-28318000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr22:28316400-28319400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:28316400-28320400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr22:28316400-28321400	Weak transcription	Spleen	Spleen
11	chr22:28316400-28322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr22:28316400-28322400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr22:28316400-28322600	Weak transcription	HSMMtube	muscle
14	chr22:28316400-28326400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr22:28316400-28326400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr22:28316400-28326400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr22:28316400-28326400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr22:28316400-28326600	Weak transcription	Right Ventricle	heart
19	chr22:28316400-28327000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr22:28316400-28328200	Weak transcription	Left Ventricle	heart
21	chr22:28316400-28329000	Weak transcription	Pancreas	Pancrea
22	chr22:28316400-28329000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr22:28316400-28335000	Weak transcription	Colonic Mucosa	Colon
24	chr22:28316400-28336800	Weak transcription	Fetal Muscle Leg	muscle
25	chr22:28316400-28342600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr22:28316400-28358600	Weak transcription	Placenta	Placenta
27	chr22:28316400-28370200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr22:28316400-28376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:28316400-28378000	Weak transcription	Esophagus	oesophagus
30	chr22:28316600-28318000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr22:28316600-28319200	Weak transcription	Fetal Thymus	thymus
32	chr22:28316600-28320000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr22:28316600-28323200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr22:28316600-28325400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr22:28316600-28328600	Weak transcription	Stomach Mucosa	stomach
36	chr22:28316600-28348400	Weak transcription	Brain Substantia Nigra	brain
37	chr22:28316800-28318000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr22:28316800-28318400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr22:28316800-28319000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr22:28316800-28319200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr22:28316800-28319200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr22:28316800-28319400	Weak transcription	Fetal Brain Female	brain
43	chr22:28316800-28320400	Weak transcription	Primary B cells from cord blood	blood
44	chr22:28316800-28320400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr22:28316800-28320400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr22:28316800-28320600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr22:28316800-28322400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr22:28316800-28325400	Weak transcription	Psoas Muscle	Psoas
49	chr22:28316800-28325800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr22:28316800-28326600	Weak transcription	Rectal Smooth Muscle	rectum

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