Variant report

Variant	rs2451753
Chromosome Location	chr6:26649018-26649019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26641377..26644016-chr6:26648888..26650401,2	K562	blood:
2	chr6:26646915..26649421-chr6:26658620..26660677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181315	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2451714	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451715	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451716	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];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451717	0.80[ASN][1000 genomes]
rs2451739	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2451742	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451746	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451749	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451752	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];1.00[ASN][1000 genomes]
rs2451754	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494691	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2494705	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494706	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494708	0.81[ASN][1000 genomes]
rs2494710	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494711	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494714	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2494715	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2498342	0.95[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2498343	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800302	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3807029	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4591839	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6902411	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6915555	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6919391	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929908	0.84[JPT][hapmap]
rs6931849	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7765920	0.85[MKK][hapmap]
rs9379892	0.84[JPT][hapmap]
rs9379902	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9379903	0.92[EUR][1000 genomes];0.82[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2451753	RP11-457M11.2	cis	Artery Tibial	GTEx
rs2451753	RP11-457M11.2	cis	lung	GTEx
rs2451753	BTN2A2	cis	cerebellum	SCAN
rs2451753	ZNF322	cis	Thyroid	GTEx
rs2451753	BTN3A2	cis	cerebellum	SCAN
rs2451753	RP11-457M11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2451753	BTN3A3	cis	cerebellum	SCAN
rs2451753	RP11-457M11.2	cis	Thyroid	GTEx
rs2451753	ZNF204P	cis	cerebellum	SCAN
rs2451753	HIST1H4L	cis	parietal	SCAN
rs2451753	BTN3A2	cis	parietal	SCAN
rs2451753	ZNF322	cis	Nerve Tibial	GTEx
rs2451753	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2451753	ZNF322	cis	Adipose Subcutaneous	GTEx
rs2451753	HIST1H3E	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26633000-26658000	Weak transcription	Fetal Brain Male	brain
2	chr6:26639000-26651800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:26641400-26659000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:26641400-26659000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:26641800-26650400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:26643400-26652000	Weak transcription	Fetal Stomach	stomach
7	chr6:26643400-26652600	Weak transcription	Ovary	ovary
8	chr6:26643400-26657600	Weak transcription	Right Ventricle	heart
9	chr6:26643400-26658800	Weak transcription	Pancreas	Pancrea
10	chr6:26643400-26659000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:26643400-26659000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:26643400-26659000	Weak transcription	Aorta	Aorta
13	chr6:26643400-26659000	Weak transcription	Lung	lung
14	chr6:26643400-26659400	Weak transcription	Esophagus	oesophagus
15	chr6:26643400-26659400	Weak transcription	Gastric	stomach
16	chr6:26643600-26654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:26643600-26655600	Weak transcription	Left Ventricle	heart
18	chr6:26643600-26657600	Weak transcription	Psoas Muscle	Psoas
19	chr6:26643600-26658000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:26643600-26658200	Weak transcription	Brain Germinal Matrix	brain
21	chr6:26643800-26650200	Weak transcription	Fetal Brain Female	brain
22	chr6:26643800-26650400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:26643800-26651000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:26643800-26657800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:26643800-26658400	Weak transcription	Fetal Heart	heart
26	chr6:26643800-26658400	Weak transcription	Small Intestine	intestine
27	chr6:26644000-26652000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:26644000-26654000	Weak transcription	Brain Anterior Caudate	brain
29	chr6:26644000-26656000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:26644000-26657600	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:26644000-26657600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:26644000-26658000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:26644000-26658000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:26644000-26658200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:26644000-26658400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:26644000-26658400	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:26644200-26650400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:26644200-26651400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:26644200-26658000	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:26644400-26651200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:26644400-26651600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:26644600-26649200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:26644600-26650200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:26644600-26653200	Weak transcription	Placenta	Placenta
45	chr6:26644600-26657600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:26644600-26658000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:26644600-26659000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:26644800-26649200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr6:26644800-26649200	Weak transcription	HSMM	muscle
50	chr6:26644800-26650200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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