Variant report

Variant	rs1555047
Chromosome Location	chr6:28328683-28328684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28328653-28328703	MCF10A-Er-Src	breast:	n/a
2	chr6:28328653-28328703	A549	lung:	n/a
3	chr6:28328653-28328703	PrEC	prostate:	n/a
4	chr6:28328653-28328703	HPAEpiC	pulmonary alveolar:	n/a
5	chr6:28328653-28328703	HRCEpiC	kidney:	n/a
6	chr6:28328653-28328703	HCF	heart:	n/a
7	chr6:28328653-28328703	HIPEpiC	eye:	n/a
8	chr6:28328653-28328703	GM12891	blood:	n/a
9	chr6:28328653-28328703	Caco-2	colon:	n/a
10	chr6:28328653-28328703	ovcar-3	ovarian:	n/a
11	chr6:28328653-28328703	CMK	blood:	n/a
12	chr6:28328653-28328703	ProgFib	skin:	n/a
13	chr6:28328653-28328703	NB4	blood:	n/a
14	chr6:28328653-28328703	H1-hESC	embryonic stem cell:	embryo
15	chr6:28328653-28328703	HRE	kidney:	n/a
16	chr6:28328653-28328703	HNPCEpiC	eye:	n/a
17	chr6:28328653-28328703	AG09309	skin:	n/a
18	chr6:28328653-28328703	MCF-7	breast:	n/a
19	chr6:28328653-28328703	LNCaP	prostate:	n/a
20	chr6:28328653-28328703	HepG2	liver:	n/a
21	chr6:28328653-28328703	NHBE	bronchial:	n/a
22	chr6:28328653-28328703	IMR90	lung:	fetal
23	chr6:28328653-28328703	PANC-1	pancreas:	n/a
24	chr6:28328653-28328703	AG04449	skin:	fetal
25	chr6:28328653-28328703	ECC-1	luminal epithelium:	n/a
26	chr6:28328653-28328703	NHDF-neo	bronchial:	n/a
27	chr6:28328653-28328703	AG10803	skin:	n/a
28	chr6:28328653-28328703	HUVEC	blood vessel:	n/a
29	chr6:28328653-28328703	K562	blood:	n/a
30	chr6:28328653-28328703	SK-N-SH_RA	brain:	n/a
31	chr6:28328653-28328703	NH-A	brain:	n/a
32	chr6:28328653-28328703	Hepatocyte	liver:	n/a
33	chr6:28328653-28328703	T-47D	breast:	n/a
34	chr6:28328653-28328703	SAEC	small airway:	n/a
35	chr6:28328653-28328703	HEK293	kidney:	embryo
36	chr6:28328653-28328703	AG04450	lung:	fetal
37	chr6:28328653-28328703	Jurkat	blood:	n/a
38	chr6:28328653-28328703	AG09319	gingival:	n/a
39	chr6:28328653-28328703	BJ	skin:	n/a
40	chr6:28328653-28328703	HCT-116	colon:	n/a
41	chr6:28328653-28328703	PFSK-1	brain:	n/a
42	chr6:28328653-28328703	BE2_C	brain:	n/a
43	chr6:28328653-28328703	SKMC	muscle:	n/a
44	chr6:28328653-28328703	U87	brain:	n/a
45	chr6:28328653-28328703	GM06990	blood:	n/a
46	chr6:28328653-28328703	HEEpiC	esophagus:	n/a
47	chr6:28328653-28328703	RPTEC	kidney:	n/a
48	chr6:28328653-28328703	GM12878	blood:	n/a
49	chr6:28328653-28328703	Hela-S3	cervix:	n/a
50	chr6:28328653-28328703	NT2-D1	testis:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:28326753..28329477-chr6:28335475..28338195,2	K562	blood:
2	chr6:28100726..28103259-chr6:28327481..28329415,2	K562	blood:
3	chr6:28323097..28326388-chr6:28326781..28330360,5	K562	blood:
4	chr6:28327846..28330234-chr6:28366542..28369079,2	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	CpG island
ENSG00000158691	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484540	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484541	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1555046	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1556957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16894121	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17313059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17313276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17314224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17314865	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314991	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17315340	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17315648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17315739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17392982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17393066	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17393342	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17393506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17393786	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17393918	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17393939	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17720687	0.82[CEU][hapmap]
rs2027362	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2072318	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2072319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs213230	0.88[CHB][hapmap]
rs213231	0.85[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2232419	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2232434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2232438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3734562	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56001748	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56241479	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56787378	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57126418	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57204212	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57366176	0.89[EUR][1000 genomes]
rs59732975	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60184496	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60660967	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6915122	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740609	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73740620	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740622	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740623	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742547	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73742550	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73742551	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73742555	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73742558	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs758396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7774788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468378	0.82[EUR][1000 genomes]
rs9717944	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:28324200-28331600	Weak transcription	Thymus	Thymus
4	chr6:28324400-28328800	Weak transcription	Brain Anterior Caudate	brain
5	chr6:28324400-28329600	Weak transcription	Aorta	Aorta
6	chr6:28324400-28329600	Weak transcription	Fetal Intestine Small	intestine
7	chr6:28324400-28330600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:28324400-28330800	Weak transcription	Brain Substantia Nigra	brain
9	chr6:28324400-28331000	Weak transcription	Psoas Muscle	Psoas
10	chr6:28324400-28331000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:28324400-28331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:28324400-28331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:28324400-28332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:28324400-28333000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:28324400-28333000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:28324400-28333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:28324400-28336000	Weak transcription	GM12878-XiMat	blood
18	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
19	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
20	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:28324600-28328800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:28324600-28329200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:28324600-28329600	Weak transcription	Pancreas	Pancrea
26	chr6:28324600-28329800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:28324600-28329800	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:28324600-28330200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr6:28324600-28330800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:28324600-28330800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:28324600-28330800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:28324600-28330800	Weak transcription	Colonic Mucosa	Colon
33	chr6:28324600-28330800	Weak transcription	Left Ventricle	heart
34	chr6:28324600-28331000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:28324600-28331000	Weak transcription	Spleen	Spleen
36	chr6:28324600-28331200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:28324600-28331200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:28324600-28331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:28324600-28331200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:28324600-28331600	Weak transcription	Fetal Kidney	kidney
41	chr6:28324600-28331800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:28324600-28332000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:28324600-28332600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:28324600-28332600	Weak transcription	Brain Angular Gyrus	brain
45	chr6:28324600-28332600	Weak transcription	HSMM	muscle
46	chr6:28324600-28332800	Weak transcription	Fetal Heart	heart
47	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:28324600-28349600	Weak transcription	NHEK	skin
49	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:28324800-28329400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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