Variant report

Variant	rs6698987
Chromosome Location	chr1:172368967-172368968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:172058604..172060338-chr1:172368296..172369500,16	MCF-7	breast:
2	chr1:172368766..172370642-chr1:172413206..172415397,2	K562	blood:
3	chr1:172010410..172011489-chr1:172368146..172369453,8	MCF-7	breast:
4	chr1:172061150..172062084-chr1:172368563..172369443,2	MCF-7	breast:
5	chr1:172368021..172370277-chr1:172372809..172374587,2	K562	blood:
6	chr1:172368697..172369321-chr1:172398135..172399069,3	MCF-7	breast:
7	chr1:172326973..172328918-chr1:172367040..172369212,2	MCF-7	breast:
8	chr1:172290820..172291829-chr1:172368303..172369352,3	MCF-7	breast:
9	chr1:172368408..172369092-chr1:172398245..172399052,2	K562	blood:
10	chr1:171971640..171972474-chr1:172368418..172369271,3	MCF-7	breast:
11	chr1:172104348..172104910-chr1:172368504..172369322,2	MCF-7	breast:
12	chr1:171971687..171972514-chr1:172368404..172369272,3	K562	blood:
13	chr1:172368576..172370246-chr1:172375053..172377189,2	MCF-7	breast:
14	chr1:172059029..172059772-chr1:172368194..172369295,4	MCF-7	breast:
15	chr1:172368428..172369228-chr1:172398285..172399043,2	MCF-7	breast:
16	chr1:172057507..172059128-chr1:172367828..172369980,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-2	chr1:172368959-172369056	NONHSAT007614
2	lnc-PIGC-2	chr1:172368959-172369056	NONHSAT007613
3	lnc-PIGC-2	chr1:172368959-172369056	NONHSAT007611
4	lnc-PIGC-2	chr1:172368959-172369056	NONHSAT007609

No data

Variant related genes	Relation type
ENSG00000135845	Chromatin interaction
ENSG00000180999	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1011731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1023479	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10489284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10752943	0.90[ASN][1000 genomes]
rs10752944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10797996	0.92[ASN][1000 genomes]
rs10911654	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10911681	0.97[ASN][1000 genomes]
rs10911684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10911792	0.90[CHB][hapmap]
rs12404665	0.92[ASN][1000 genomes]
rs12405515	0.85[ASN][1000 genomes]
rs1894633	0.89[CHB][hapmap]
rs2001127	0.95[ASN][1000 genomes]
rs2001128	0.95[ASN][1000 genomes]
rs2001129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2032528	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2213731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2213732	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2227198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2227199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2227200	0.90[ASN][1000 genomes]
rs2269612	0.92[ASN][1000 genomes]
rs2301453	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3213564	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3768445	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4471302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4504922	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4916251	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4916252	0.92[ASN][1000 genomes]
rs4916253	0.95[ASN][1000 genomes]
rs4916254	0.88[ASN][1000 genomes]
rs4916263	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916264	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916265	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs6424894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6676665	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6700575	0.97[ASN][1000 genomes]
rs714515	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7517737	0.89[ASN][1000 genomes]
rs7518039	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7539464	0.95[ASN][1000 genomes]
rs7539972	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7544610	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7546252	0.95[ASN][1000 genomes]
rs9286854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425269	1.00[JPT][hapmap]
rs9425291	0.89[CHB][hapmap]
rs9425297	0.94[ASN][1000 genomes]
rs9425298	0.95[ASN][1000 genomes]
rs9425299	0.95[ASN][1000 genomes]
rs9425300	0.95[ASN][1000 genomes]
rs9425301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9425579	0.93[ASN][1000 genomes]
rs9425586	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425587	0.92[ASN][1000 genomes]
rs9425589	0.92[ASN][1000 genomes]
rs9425590	0.92[ASN][1000 genomes]
rs9425591	0.95[ASN][1000 genomes]
rs9425592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425628	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs979935	0.89[CHB][hapmap]
rs991790	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172352400-172386400	Weak transcription	Psoas Muscle	Psoas
2	chr1:172360200-172369200	Weak transcription	Spleen	Spleen
3	chr1:172360600-172369000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:172360600-172369200	Weak transcription	Small Intestine	intestine
5	chr1:172362400-172369200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:172363800-172369200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:172364000-172369200	Weak transcription	Placenta	Placenta
8	chr1:172365800-172370000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:172366200-172369200	Enhancers	HUVEC	blood vessel
10	chr1:172366200-172369600	Enhancers	Brain Angular Gyrus	brain
11	chr1:172366200-172369800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:172366200-172370200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:172366200-172370200	Enhancers	NH-A	brain
14	chr1:172366400-172369200	Enhancers	Fetal Heart	heart
15	chr1:172366400-172369400	Enhancers	HMEC	breast
16	chr1:172366400-172369600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:172366600-172369600	Enhancers	HSMM	muscle
18	chr1:172366800-172371200	Enhancers	Rectal Smooth Muscle	rectum
19	chr1:172367000-172369600	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:172367000-172370600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:172367000-172372800	Enhancers	Primary T cells from cord blood	blood
22	chr1:172367200-172369800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:172367200-172370800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:172367200-172370800	Enhancers	Fetal Stomach	stomach
25	chr1:172367200-172372000	Enhancers	Fetal Lung	lung
26	chr1:172367400-172369600	Enhancers	Fetal Intestine Small	intestine
27	chr1:172367600-172369200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:172367600-172369400	Enhancers	NHLF	lung
29	chr1:172367600-172370600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:172367600-172370800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:172367800-172369400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr1:172367800-172369600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:172367800-172369800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:172367800-172370200	Enhancers	HSMMtube	muscle
35	chr1:172368000-172369600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:172368000-172369800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:172368000-172370200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:172368200-172369000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:172368200-172369400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:172368200-172369400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr1:172368200-172369600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:172368200-172369800	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr1:172368200-172370200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:172368200-172370800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr1:172368400-172369200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:172368400-172369400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:172368400-172369400	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:172368400-172369600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:172368400-172369800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr1:172368400-172370200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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