Variant report

Variant	rs974963
Chromosome Location	chr6:30314567-30314568
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr6:30314400-30314685	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:30311254-30314649	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30314540-30314590	ovcar-3	ovarian:	n/a
2	chr6:30314540-30314590	HRE	kidney:	n/a
3	chr6:30314540-30314590	A549	lung:	n/a
4	chr6:30314540-30314590	Hepatocyte	liver:	n/a
5	chr6:30314540-30314590	NH-A	brain:	n/a
6	chr6:30314540-30314590	NHDF-neo	bronchial:	n/a
7	chr6:30314540-30314590	HCF	heart:	n/a
8	chr6:30314540-30314590	BJ	skin:	n/a
9	chr6:30314540-30314590	Jurkat	blood:	n/a
10	chr6:30314540-30314590	SK-N-SH	brain:	n/a
11	chr6:30314540-30314590	HepG2	liver:	n/a
12	chr6:30314540-30314590	SKMC	muscle:	n/a
13	chr6:30314540-30314590	ECC-1	luminal epithelium:	n/a
14	chr6:30314540-30314590	AG09309	skin:	n/a
15	chr6:30314540-30314590	Hela-S3	cervix:	n/a
16	chr6:30314540-30314590	SAEC	small airway:	n/a
17	chr6:30314540-30314590	PFSK-1	brain:	n/a
18	chr6:30314540-30314590	HRPEpiC	eye:	n/a
19	chr6:30314540-30314590	HIPEpiC	eye:	n/a
20	chr6:30314540-30314590	AG09319	gingival:	n/a
21	chr6:30314540-30314590	PrEC	prostate:	n/a
22	chr6:30314540-30314590	HRCEpiC	kidney:	n/a
23	chr6:30314540-30314590	H1-hESC	embryonic stem cell:	embryo
24	chr6:30314540-30314590	HNPCEpiC	eye:	n/a
25	chr6:30314540-30314590	HEEpiC	esophagus:	n/a
26	chr6:30314540-30314590	IMR90	lung:	fetal
27	chr6:30314540-30314590	RPTEC	kidney:	n/a
28	chr6:30314540-30314590	PANC-1	pancreas:	n/a
29	chr6:30314540-30314590	SK-N-MC	brain:	n/a
30	chr6:30314540-30314590	HMEC	breast:	n/a
31	chr6:30314540-30314590	HEK293	kidney:	embryo
32	chr6:30314540-30314590	HL-60	blood:	n/a
33	chr6:30314540-30314590	GM19239	blood:	n/a
34	chr6:30314540-30314590	CMK	blood:	n/a
35	chr6:30314540-30314590	K562	blood:	n/a
36	chr6:30314540-30314590	AG10803	skin:	n/a
37	chr6:30314540-30314590	AG04450	lung:	fetal
38	chr6:30314540-30314590	MCF10A-Er-Src	breast:	n/a
39	chr6:30314540-30314590	SK-N-SH_RA	brain:	n/a
40	chr6:30314540-30314590	NT2-D1	testis:	n/a
41	chr6:30314540-30314590	T-47D	breast:	n/a
42	chr6:30314540-30314590	U87	brain:	n/a
43	chr6:30314540-30314590	NHBE	bronchial:	n/a
44	chr6:30314540-30314590	MCF-7	breast:	n/a
45	chr6:30314540-30314590	HPAEpiC	pulmonary alveolar:	n/a
46	chr6:30314540-30314590	HCM	heart:	n/a
47	chr6:30314540-30314590	BE2_C	brain:	n/a
48	chr6:30314540-30314590	NB4	blood:	n/a
49	chr6:30314540-30314590	HUVEC	blood vessel:	n/a
50	chr6:30314540-30314590	GM12878	blood:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30178310..30184484-chr6:30311860..30320436,13	MCF-7	breast:
2	chr20:55838873..55840993-chr6:30313290..30315542,2	MCF-7	breast:
3	chr6:30188017..30189614-chr6:30314561..30316760,2	MCF-7	breast:
4	chr6:30170658..30173210-chr6:30313081..30315587,2	K562	blood:
5	chr6:30314566..30317004-chr6:30328728..30331075,2	MCF-7	breast:
6	chr6:30293058..30297784-chr6:30308514..30315279,24	MCF-7	breast:

No data

Variant related genes	Relation type
HLA-N	TF binding region
HLA-N	CpG island
ENSG00000248167	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000231074	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1045251	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060065	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1264616	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1473102	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2023476	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2023477	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2023478	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2057727	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2074474	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2097773	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2394780	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2508026	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2516697	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2516699	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516700	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516702	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516704	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516705	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516706	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2516707	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516710	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516713	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2523737	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2523744	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2523745	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2523746	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2523747	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2523748	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523750	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs261943	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs261948	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs261949	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28360021	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28360023	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844752	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844761	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844763	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2844765	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3778624	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6904208	0.81[AFR][1000 genomes]
rs6912239	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6912495	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7452694	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7767817	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295843	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380168	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380174	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9394001	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394003	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs962899	0.93[EUR][1000 genomes];0.84[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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs974963	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs974963	RPP21	cis	multi-tissue	Pritchard
rs974963	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs974963	HCG18	cis	normal skin	skin_eQTL
rs974963	LOC401245	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30313400-30321400	Weak transcription	Spleen	Spleen
2	chr6:30313800-30314600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:30313800-30316400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:30313800-30325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:30314000-30314600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:30314000-30314600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:30314000-30314600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:30314000-30314600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:30314000-30314800	Strong transcription	HSMMtube	muscle
10	chr6:30314000-30315000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:30314000-30315000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:30314000-30315400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:30314000-30316400	Weak transcription	Adipose Nuclei	Adipose
14	chr6:30314000-30316400	Strong transcription	Thymus	Thymus
15	chr6:30314000-30316800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:30314000-30317200	Weak transcription	Brain Substantia Nigra	brain
17	chr6:30314000-30318000	Weak transcription	Fetal Kidney	kidney
18	chr6:30314000-30318400	Weak transcription	HSMM	muscle
19	chr6:30314000-30319400	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:30314000-30319400	Weak transcription	Colonic Mucosa	Colon
21	chr6:30314000-30323200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:30314000-30323200	Weak transcription	Aorta	Aorta
23	chr6:30314000-30324200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:30314000-30325600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:30314200-30314600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:30314200-30314600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:30314200-30314600	Genic enhancers	Fetal Brain Female	brain
28	chr6:30314200-30314600	Genic enhancers	Dnd41	blood
29	chr6:30314200-30314800	Weak transcription	Gastric	stomach
30	chr6:30314200-30314800	Strong transcription	NHLF	lung
31	chr6:30314200-30315000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:30314200-30315000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:30314200-30315000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:30314200-30315000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:30314200-30315000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr6:30314200-30315000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr6:30314200-30315000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr6:30314200-30315000	Strong transcription	Fetal Thymus	thymus
39	chr6:30314200-30315000	Strong transcription	Ovary	ovary
40	chr6:30314200-30315000	Strong transcription	HMEC	breast
41	chr6:30314200-30315200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:30314200-30315200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:30314200-30315200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:30314200-30315200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:30314200-30315200	Strong transcription	Brain Cingulate Gyrus	brain
46	chr6:30314200-30315200	Strong transcription	Placenta	Placenta
47	chr6:30314200-30315400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:30314200-30315400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:30314200-30315400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:30314200-30315400	Strong transcription	Stomach Smooth Muscle	stomach

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