Variant report

Variant	rs6676545
Chromosome Location	chr1:151611948-151611949
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151585204..151586815-chr1:151610072..151612595,2	K562	blood:
2	chr1:151583806..151586204-chr1:151610936..151612672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143376	Chromatin interaction
ENSG00000250734	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12733147	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12745172	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12746897	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12751044	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12752221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1607933	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];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17641780	0.90[JPT][hapmap]
rs2280475	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3204344	0.95[JPT][hapmap]
rs35388624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35654949	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828056	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4466658	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs56130043	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58983661	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6685067	0.95[JPT][hapmap]
rs6687866	0.95[JPT][hapmap]
rs6690942	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs6702842	0.95[JPT][hapmap]

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	nsv2843	chr1:151600069-151644709	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6676545	TDRKH	cis	cerebellum	SCAN
rs6676545	SPRR2B	cis	cerebellum	SCAN
rs6676545	SLC27A3	cis	cerebellum	SCAN
rs6676545	GATAD2B	cis	cerebellum	SCAN
rs6676545	LINGO4	cis	cerebellum	SCAN
rs6676545	VPS45	cis	cerebellum	SCAN
rs6676545	NPR1	cis	cerebellum	SCAN
rs6676545	LCE1C	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151586400-151622200	Weak transcription	Fetal Thymus	thymus
2	chr1:151586400-151626600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:151587600-151640600	Weak transcription	Fetal Brain Male	brain
4	chr1:151588000-151626600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:151588200-151620600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:151588200-151665200	Weak transcription	Aorta	Aorta
7	chr1:151589000-151617600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:151589000-151620600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:151589600-151613200	Weak transcription	Dnd41	blood
10	chr1:151591000-151630800	Weak transcription	Fetal Kidney	kidney
11	chr1:151591200-151675400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:151592000-151622600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:151592600-151613200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:151592600-151613600	Weak transcription	NHEK	skin
15	chr1:151592600-151613800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:151592600-151633800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:151592800-151630600	Weak transcription	Hela-S3	cervix
18	chr1:151593600-151612600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:151594000-151612400	Weak transcription	HSMM	muscle
20	chr1:151594000-151621000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:151594000-151652800	Weak transcription	Right Ventricle	heart
22	chr1:151594200-151617400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:151594200-151620600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:151594600-151613200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:151597800-151616200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:151598400-151613400	Weak transcription	Placenta	Placenta
27	chr1:151601200-151617800	Weak transcription	Fetal Brain Female	brain
28	chr1:151601400-151612000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:151601400-151629800	Weak transcription	Thymus	Thymus
30	chr1:151601600-151613200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:151603000-151663200	Weak transcription	Colonic Mucosa	Colon
32	chr1:151606000-151621800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:151606200-151612600	Enhancers	Colon Smooth Muscle	Colon
34	chr1:151606800-151630800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:151608000-151612600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:151608200-151615000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:151608200-151630600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:151608600-151613400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:151608800-151612600	Enhancers	Rectal Smooth Muscle	rectum
40	chr1:151609800-151612800	Enhancers	NH-A	brain
41	chr1:151610000-151612200	Enhancers	Small Intestine	intestine
42	chr1:151610000-151612600	Enhancers	Stomach Mucosa	stomach
43	chr1:151610000-151612800	Enhancers	NHLF	lung
44	chr1:151610200-151612600	Enhancers	HepG2	liver
45	chr1:151610200-151612800	Enhancers	Fetal Intestine Small	intestine
46	chr1:151610200-151633800	Weak transcription	HUVEC	blood vessel
47	chr1:151610400-151612000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:151610400-151612000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr1:151610400-151612400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:151610400-151612800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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