Variant report

Variant	rs13253942
Chromosome Location	chr8:126154649-126154650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:126153172..126155886-chr8:126160389..126162801,2	K562	blood:
2	chr8:126151658..126158351-chr8:126441101..126448001,9	MCF-7	breast:
3	chr8:126154610..126158392-chr8:126442240..126446701,5	MCF-7	breast:
4	chr8:126151269..126152960-chr8:126154385..126157125,2	MCF-7	breast:
5	chr8:126147294..126149147-chr8:126153255..126155156,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173334	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs12675943	0.83[EUR][1000 genomes]
rs12681602	0.81[CEU][hapmap]
rs13249982	0.90[CEU][hapmap]
rs13254947	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13259062	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13262348	0.95[ASN][1000 genomes]
rs13264500	0.92[EUR][1000 genomes]
rs13267325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13273034	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13273231	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13273421	0.88[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13277490	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13279146	1.00[ASW][hapmap]
rs16900452	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17310558	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17318327	1.00[ASW][hapmap]
rs17401283	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403341	1.00[ASW][hapmap]
rs2384882	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34110249	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34246020	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34298715	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34427316	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34448805	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34461511	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34694976	0.95[ASN][1000 genomes]
rs34737949	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34903473	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033076	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35140299	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35215140	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35336507	0.84[EUR][1000 genomes]
rs35401436	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35475899	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35564243	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35774093	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35822368	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35861494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35955519	0.84[EUR][1000 genomes]
rs35991395	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081564	1.00[ASN][1000 genomes]
rs3923300	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4360308	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477044	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4601329	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4871570	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.95[ASN][1000 genomes]
rs56135036	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66561774	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66826725	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66929016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71516763	0.92[ASN][1000 genomes]
rs71516769	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72720550	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7461756	0.90[CEU][hapmap]
rs868227	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv949614	chr8:126063646-126376699	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv917158	chr8:126101990-126255266	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	nsv1022954	chr8:126117811-126180331	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13253942	CCR1	trans	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126105200-126156400	Weak transcription	Fetal Brain Male	brain
2	chr8:126117600-126157400	Weak transcription	Fetal Brain Female	brain
3	chr8:126117800-126160400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr8:126118000-126191800	Weak transcription	Thymus	Thymus
5	chr8:126120600-126156400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:126137600-126158400	Weak transcription	Placenta	Placenta
7	chr8:126137600-126213600	Weak transcription	Fetal Stomach	stomach
8	chr8:126138000-126163000	Weak transcription	Fetal Kidney	kidney
9	chr8:126138000-126163600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr8:126138000-126191000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr8:126138000-126197800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr8:126138200-126156000	Weak transcription	Aorta	Aorta
13	chr8:126138200-126156400	Weak transcription	Esophagus	oesophagus
14	chr8:126138200-126158000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr8:126138200-126160200	Weak transcription	Spleen	Spleen
16	chr8:126138200-126170400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr8:126138200-126200400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:126138400-126200200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr8:126140400-126162200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:126141000-126155800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr8:126141000-126156200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr8:126141600-126156400	Weak transcription	Lung	lung
23	chr8:126141600-126156400	Weak transcription	Small Intestine	intestine
24	chr8:126141600-126159800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr8:126142600-126155200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr8:126142600-126163000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr8:126142600-126231400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr8:126142800-126156600	Weak transcription	Liver	Liver
29	chr8:126142800-126162000	Weak transcription	HSMM	muscle
30	chr8:126143000-126155800	Weak transcription	NH-A	brain
31	chr8:126143000-126193200	Weak transcription	Left Ventricle	heart
32	chr8:126143200-126155800	Weak transcription	K562	blood
33	chr8:126143200-126158000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr8:126143200-126162200	Weak transcription	GM12878-XiMat	blood
35	chr8:126143200-126180600	Weak transcription	Fetal Muscle Leg	muscle
36	chr8:126143200-126186800	Weak transcription	Adipose Nuclei	Adipose
37	chr8:126143400-126156200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:126143400-126156600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:126143400-126162200	Weak transcription	HSMMtube	muscle
40	chr8:126143400-126163800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr8:126143600-126156400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr8:126143600-126160200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr8:126143800-126155200	Weak transcription	HUVEC	blood vessel
44	chr8:126143800-126157800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr8:126143800-126160000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr8:126143800-126163800	Weak transcription	Fetal Lung	lung
47	chr8:126144200-126156400	Weak transcription	Brain Anterior Caudate	brain
48	chr8:126144200-126156400	Weak transcription	Fetal Thymus	thymus
49	chr8:126144200-126156600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr8:126144200-126157800	Weak transcription	Primary monocytes fromperipheralblood	blood

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