Variant report

Variant	rs1322815
Chromosome Location	chr6:109704062-109704063
allele	C/T
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	POLR2A	chr6:109702460-109704704	GM12892	blood:	n/a	n/a
2	POLR2A	chr6:109703020-109704359	A549	lung:	n/a	n/a
3	USF1	chr6:109703196-109704662	K562	blood:	n/a	chr6:109703691-109703712 chr6:109703695-109703708 chr6:109703696-109703705 chr6:109703697-109703706 chr6:109703697-109703706
4	MYC	chr6:109703150-109704441	MCF-7	breast:	n/a	chr6:109704234-109704247 chr6:109704025-109704034 chr6:109704234-109704249 chr6:109704236-109704245 chr6:109703697-109703706 chr6:109704235-109704246 chr6:109704232-109704247 chr6:109704237-109704246 chr6:109704236-109704246 chr6:109704236-109704246 chr6:109704025-109704038 chr6:109704026-109704037 chr6:109704235-109704246 chr6:109704234-109704247 chr6:109704235-109704245 chr6:109704027-109704036 chr6:109704236-109704246
5	MAFK	chr6:109703455-109704795	K562	blood:	n/a	n/a
6	TAF1	chr6:109702747-109704679	H1-hESC	embryonic stem cell:	n/a	n/a
7	HEY1	chr6:109703792-109704608	HepG2	liver:	n/a	n/a
8	RUNX3	chr6:109702179-109704771	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:109702702-109704642	GM15510	blood:	n/a	n/a
10	ELF1	chr6:109703557-109704487	HepG2	liver:	n/a	n/a
11	USF2	chr6:109703500-109704407	HepG2	liver:	n/a	chr6:109703691-109703712 chr6:109703695-109703708 chr6:109703696-109703705 chr6:109703697-109703706 chr6:109703697-109703706
12	POLR2A	chr6:109701931-109705038	GM12891	blood:	n/a	n/a
13	USF1	chr6:109703391-109704529	A549	lung:	n/a	chr6:109703691-109703712 chr6:109703695-109703708 chr6:109703696-109703705 chr6:109703697-109703706 chr6:109703697-109703706
14	CREB1	chr6:109703020-109704844	K562	blood:	n/a	n/a
15	POLR2A	chr6:109702612-109704685	K562	blood:	n/a	n/a
16	POLR2A	chr6:109703907-109704523	HepG2	liver:	n/a	n/a
17	CEBPB	chr6:109703796-109704604	A549	lung:	n/a	n/a
18	BHLHE40	chr6:109703453-109704135	A549	lung:	n/a	chr6:109703691-109703712 chr6:109703695-109703708 chr6:109703696-109703705 chr6:109703697-109703706 chr6:109703697-109703706
19	NFATC1	chr6:109703804-109704698	GM12878	blood:	n/a	n/a
20	E2F6	chr6:109703400-109704539	A549	lung:	n/a	chr6:109703561-109703572
21	EP300	chr6:109703346-109704652	GM12878	blood:	n/a	chr6:109703356-109703372 chr6:109703652-109703661
22	TFAP2C	chr6:109702658-109704663	Hela-S3	cervix:	n/a	chr6:109704302-109704317
23	USF1	chr6:109703247-109704587	ECC-1	luminal epithelium:	n/a	chr6:109703691-109703712 chr6:109703695-109703708 chr6:109703696-109703705 chr6:109703697-109703706 chr6:109703697-109703706
24	TAL1	chr6:109702272-109704867	K562	blood:	n/a	n/a
25	POLR2A	chr6:109702590-109704801	HUVEC	blood vessel:	n/a	n/a
26	SIN3AK20	chr6:109703933-109704646	HepG2	liver:	n/a	n/a
27	MAX	chr6:109702806-109704674	K562	blood:	n/a	chr6:109704234-109704247 chr6:109704025-109704034 chr6:109704234-109704249 chr6:109704236-109704245 chr6:109703697-109703706 chr6:109704235-109704246 chr6:109704232-109704247 chr6:109704237-109704246 chr6:109704236-109704246 chr6:109704236-109704246 chr6:109704025-109704038 chr6:109704026-109704037 chr6:109704235-109704246 chr6:109704234-109704247 chr6:109704235-109704245 chr6:109704027-109704036 chr6:109704236-109704246
28	EGR1	chr6:109703402-109704555	ECC-1	luminal epithelium:	n/a	chr6:109703722-109703737 chr6:109703726-109703736 chr6:109703723-109703736 chr6:109703726-109703735 chr6:109703723-109703736 chr6:109703654-109703664 chr6:109703723-109703736 chr6:109703723-109703736 chr6:109703723-109703737
29	YY1	chr6:109704059-109704603	H1-hESC	embryonic stem cell:	n/a	n/a
30	E2F6	chr6:109702893-109704555	K562	blood:	n/a	chr6:109703561-109703572 chr6:109703375-109703387
31	SP1	chr6:109703574-109704666	GM12878	blood:	n/a	chr6:109703780-109703794 chr6:109703739-109703753 chr6:109703742-109703753
32	POLR2A	chr6:109702798-109704625	HUVEC	blood vessel:	n/a	n/a
33	CEBPB	chr6:109703514-109704575	HepG2	liver:	n/a	n/a
34	POLR2A	chr6:109702006-109705187	IMR90	lung:	n/a	n/a
35	NRF1	chr6:109703476-109704503	GM12878	blood:	n/a	n/a
36	CTCF	chr6:109703755-109705046	HCT-116	colon:	n/a	chr6:109704592-109704610 chr6:109704587-109704608 chr6:109704593-109704609
37	FOXA1	chr6:109703402-109704124	HepG2	liver:	n/a	n/a
38	RELA	chr6:109703450-109704914	GM19193	blood:	n/a	n/a
39	MYC	chr6:109702927-109704757	Hela-S3	cervix:	n/a	chr6:109704234-109704247 chr6:109704025-109704034 chr6:109704234-109704249 chr6:109704236-109704245 chr6:109703697-109703706 chr6:109704235-109704246 chr6:109704232-109704247 chr6:109704237-109704246 chr6:109704236-109704246 chr6:109704236-109704246 chr6:109704025-109704038 chr6:109704026-109704037 chr6:109704235-109704246 chr6:109704234-109704247 chr6:109704235-109704245 chr6:109704027-109704036 chr6:109704236-109704246
40	POLR2A	chr6:109702633-109704704	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr6:109703929-109704304	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr6:109703880-109704167	A549	lung:	n/a	n/a
43	SIN3A	chr6:109702357-109704764	H1-hESC	embryonic stem cell:	n/a	chr6:109703696-109703705 chr6:109704028-109704037 chr6:109704026-109704035
44	RFX5	chr6:109703486-109704723	GM12878	blood:	n/a	n/a
45	ETS1	chr6:109703885-109704511	K562	blood:	n/a	n/a
46	POLR2A	chr6:109703030-109704839	PFSK-1	brain:	n/a	n/a
47	NFATC1	chr6:109703415-109704690	GM12878	blood:	n/a	n/a
48	ZNF143	chr6:109703337-109704707	H1-hESC	embryonic stem cell:	n/a	n/a
49	SP1	chr6:109703262-109704594	A549	lung:	n/a	chr6:109703780-109703794 chr6:109703739-109703753 chr6:109703742-109703753
50	POLR2A	chr6:109703826-109704657	HUVEC	blood vessel:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:109704021-109704071	LNCaP	prostate:	n/a
2	chr6:109704021-109704071	SK-N-SH_RA	brain:	n/a
3	chr6:109704021-109704071	GM12878	blood:	n/a
4	chr6:109704021-109704071	HCM	heart:	n/a
5	chr6:109704021-109704071	SK-N-SH	brain:	n/a
6	chr6:109704021-109704071	MCF-7	breast:	n/a
7	chr6:109704021-109704071	IMR90	lung:	fetal
8	chr6:109704021-109704071	PANC-1	pancreas:	n/a
9	chr6:109704021-109704071	Hepatocyte	liver:	n/a
10	chr6:109704021-109704071	HRCEpiC	kidney:	n/a
11	chr6:109704021-109704071	HNPCEpiC	eye:	n/a
12	chr6:109704021-109704071	U87	brain:	n/a
13	chr6:109704021-109704071	T-47D	breast:	n/a
14	chr6:109704021-109704071	Jurkat	blood:	n/a
15	chr6:109704021-109704071	HCF	heart:	n/a
16	chr6:109704021-109704071	SK-N-MC	brain:	n/a
17	chr6:109704021-109704071	RPTEC	kidney:	n/a
18	chr6:109704021-109704071	HRE	kidney:	n/a
19	chr6:109704021-109704071	A549	lung:	n/a
20	chr6:109704021-109704071	AG04450	lung:	fetal
21	chr6:109704021-109704071	H1-hESC	embryonic stem cell:	embryo
22	chr6:109704021-109704071	AG10803	skin:	n/a
23	chr6:109704021-109704071	MCF10A-Er-Src	breast:	n/a
24	chr6:109704021-109704071	HCT-116	colon:	n/a
25	chr6:109704021-109704071	HAEpiC	amniotic membrane:	n/a
26	chr6:109704021-109704071	HMEC	breast:	n/a
27	chr6:109704021-109704071	HIPEpiC	eye:	n/a
28	chr6:109704021-109704071	NHBE	bronchial:	n/a
29	chr6:109704021-109704071	NHDF-neo	bronchial:	n/a
30	chr6:109704021-109704071	SAEC	small airway:	n/a
31	chr6:109704021-109704071	HL-60	blood:	n/a
32	chr6:109704021-109704071	K562	blood:	n/a
33	chr6:109704021-109704071	GM19239	blood:	n/a
34	chr6:109704021-109704071	HPAEpiC	pulmonary alveolar:	n/a
35	chr6:109704021-109704071	HUVEC	blood vessel:	n/a
36	chr6:109704021-109704071	HCPEpiC	choroid plexus:	n/a
37	chr6:109704021-109704071	Caco-2	colon:	n/a
38	chr6:109704021-109704071	NT2-D1	testis:	n/a
39	chr6:109704021-109704071	Hela-S3	cervix:	n/a
40	chr6:109704021-109704071	AG09309	skin:	n/a
41	chr6:109704021-109704071	BE2_C	brain:	n/a
42	chr6:109704021-109704071	AG04449	skin:	fetal
43	chr6:109704021-109704071	PFSK-1	brain:	n/a
44	chr6:109704021-109704071	HRPEpiC	eye:	n/a
45	chr6:109704021-109704071	NB4	blood:	n/a
46	chr6:109704021-109704071	GM06990	blood:	n/a
47	chr6:109704021-109704071	AoSMC	blood vessel:	n/a
48	chr6:109704021-109704071	HepG2	liver:	n/a
49	chr6:109704021-109704071	SKMC	muscle:	n/a
50	chr6:109704021-109704071	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:109414172..109420012-chr6:109700263..109705604,12	MCF-7	breast:
2	chr6:109613797..109616312-chr6:109702118..109704634,2	MCF-7	breast:
3	chr6:109703058..109705958-chr6:109774873..109777253,2	MCF-7	breast:
4	chr6:109169591..109171357-chr6:109702738..109704279,2	MCF-7	breast:
5	chr1:156023965..156024660-chr6:109703764..109704584,2	Hela-S3	cervix:
6	chr6:109703226..109705290-chr6:109802868..109805423,2	K562	blood:
7	chr6:109554938..109560362-chr6:109702019..109707132,8	K562	blood:
8	chr6:109415709..109416439-chr6:109703716..109704341,2	Hela-S3	cervix:
9	chr6:109702383..109706611-chr6:109760202..109762116,4	K562	blood:
10	chr1:28907885..28908786-chr6:109703619..109704576,2	Hela-S3	cervix:
11	chr6:109414769..109417470-chr6:109702121..109705671,6	MCF-7	breast:
12	chr6:108878269..108881845-chr6:109702991..109706559,3	K562	blood:
13	chr6:109414834..109419474-chr6:109701430..109708028,12	K562	blood:
14	chr19:12902264..12902774-chr6:109703215..109704201,2	Hela-S3	cervix:
15	chr6:109556893..109560362-chr6:109702019..109704753,3	K562	blood:
16	chr6:109702597..109705942-chr6:109803330..109806291,3	K562	blood:
17	chr6:109702022..109707287-chr6:109760251..109763953,8	MCF-7	breast:
18	chr6:109702065..109705528-chr6:109760483..109765471,8	MCF-7	breast:
19	chr6:109703037..109705174-chr6:109776212..109778845,2	K562	blood:
20	chr6:109624351..109631970-chr6:109702157..109706422,11	K562	blood:
21	chr15:49103155..49104100-chr6:109703791..109704391,2	Hela-S3	cervix:
22	chr6:109610868..109612861-chr6:109702210..109704800,2	K562	blood:
23	chr6:109414590..109417855-chr6:109700035..109707147,9	K562	blood:
24	chr6:109623091..109628183-chr6:109700606..109706462,9	K562	blood:
25	chr6:109659415..109661984-chr6:109702237..109705687,4	MCF-7	breast:
26	chr6:109508327..109509699-chr6:109704031..109705079,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMPD2-1	chr6:109703998-109704869	ENSG00000260273.1

Variant related genes	Relation type
CD164	TF binding region
CD164	CpG island
ENSG00000116586	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000118689	Chromatin interaction
ENSG00000219700	Chromatin interaction
ENSG00000243587	Chromatin interaction
ENSG00000197989	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000238474	Chromatin interaction
ENSG00000201023	Chromatin interaction
ENSG00000103995	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000203799	Chromatin interaction
ENSG00000118690	Chromatin interaction
ENSG00000135596	Chromatin interaction
ENSG00000112365	Chromatin interaction
ENSG00000135587	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1054607	0.87[GIH][hapmap]
rs12175588	0.95[CEU][hapmap];0.94[JPT][hapmap]
rs12194431	0.91[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1321208	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs17070494	1.00[YRI][hapmap]
rs2884037	0.81[JPT][hapmap]
rs6920712	0.86[GIH][hapmap]
rs752261	1.00[LWK][hapmap]
rs7757895	0.91[CEU][hapmap];0.80[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs9372213	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9384712	0.91[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9480980	0.91[CEU][hapmap];0.94[JPT][hapmap]
rs9487132	0.86[CEU][hapmap]
rs9766863	0.86[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1322815	AKD1	cis	cerebellum	SCAN
rs1322815	RFPL4B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109700200-109705600	Active TSS	Stomach Smooth Muscle	stomach
2	chr6:109700400-109705200	Active TSS	Right Ventricle	heart
3	chr6:109700600-109704800	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:109700600-109704800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:109700600-109704800	Active TSS	Fetal Intestine Small	intestine
6	chr6:109700600-109704800	Active TSS	Fetal Muscle Leg	muscle
7	chr6:109700600-109704800	Active TSS	GM12878-XiMat	blood
8	chr6:109700600-109705000	Active TSS	Left Ventricle	heart
9	chr6:109700600-109705800	Active TSS	Ovary	ovary
10	chr6:109700600-109706000	Active TSS	Colonic Mucosa	Colon
11	chr6:109700600-109706200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr6:109700800-109704800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:109700800-109704800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:109700800-109704800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:109700800-109704800	Active TSS	Primary T cells fromperipheralblood	blood
16	chr6:109700800-109704800	Active TSS	Fetal Intestine Large	intestine
17	chr6:109700800-109704800	Active TSS	NHLF	lung
18	chr6:109700800-109705800	Active TSS	Psoas Muscle	Psoas
19	chr6:109701000-109704600	Active TSS	Fetal Thymus	thymus
20	chr6:109701000-109704600	Active TSS	Hela-S3	cervix
21	chr6:109701000-109705000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:109701200-109704600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:109701200-109704800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:109701200-109704800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:109701200-109704800	Active TSS	Stomach Mucosa	stomach
26	chr6:109701200-109705200	Active TSS	Fetal Muscle Trunk	muscle
27	chr6:109701400-109704600	Active TSS	Aorta	Aorta
28	chr6:109701400-109704600	Active TSS	Small Intestine	intestine
29	chr6:109701400-109704800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:109701400-109704800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:109701400-109704800	Active TSS	Placenta	Placenta
32	chr6:109701400-109704800	Active TSS	NHDF-Ad	bronchial
33	chr6:109701400-109705200	Active TSS	H1 Cell Line	embryonic stem cell
34	chr6:109701400-109705600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:109701600-109704600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:109701600-109704600	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr6:109701600-109704600	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr6:109701600-109704600	Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:109701600-109704600	Active TSS	Duodenum Mucosa	Duodenum
40	chr6:109701600-109704600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr6:109701600-109704800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:109701600-109704800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:109701600-109704800	Active TSS	Adipose Nuclei	Adipose
44	chr6:109701600-109704800	Active TSS	Brain Substantia Nigra	brain
45	chr6:109701600-109704800	Active TSS	Colon Smooth Muscle	Colon
46	chr6:109701600-109704800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr6:109701600-109704800	Active TSS	Fetal Stomach	stomach
48	chr6:109701600-109704800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr6:109701600-109704800	Active TSS	Thymus	Thymus
50	chr6:109701600-109704800	Active TSS	HMEC	breast

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