Variant report

Variant	rs6927168
Chromosome Location	chr6:166745394-166745395
allele	C/G
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	chr6:166742700-166754624	K562	blood:	n/a	n/a
2	POLR2A	chr6:166745300-166754633	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:166738156..166741727-chr6:166741924..166746289,6	K562	blood:
2	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:
3	chr6:166744901..166745588-chr6:166814062..166814853,2	K562	blood:
4	chr6:166745230..166747762-chr6:166754729..166756977,2	MCF-7	breast:

Variant related genes	Relation type
SFT2D1	TF binding region
HNRNPA1P49	TF binding region
ENSG00000060762	Chromatin interaction
ENSG00000198818	Chromatin interaction
ENSG00000261420	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10806847	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10862	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2343590	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4470829	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4598048	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4709112	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4710041	0.82[AMR][1000 genomes]
rs6909951	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6918901	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7757549	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355572	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9356476	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9366005	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366006	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9366007	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9459654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6927168	HNRNPA1P49	cis	lung	GTEx
rs6927168	SFT2D1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
4	chr6:166733800-166749600	Weak transcription	Psoas Muscle	Psoas
5	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
6	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
7	chr6:166737000-166745600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:166738200-166754200	Weak transcription	NH-A	brain
9	chr6:166739400-166745400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:166739400-166746800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:166739400-166748000	Weak transcription	Gastric	stomach
12	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:166740000-166750800	Weak transcription	HSMMtube	muscle
14	chr6:166740400-166748600	Weak transcription	Brain Germinal Matrix	brain
15	chr6:166741400-166746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:166741400-166750000	Weak transcription	HMEC	breast
17	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:166741600-166746400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:166742200-166746600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:166742200-166751200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:166742400-166748200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:166742600-166745600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:166742600-166746200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:166742600-166746400	Weak transcription	Placenta	Placenta
25	chr6:166742600-166746400	Weak transcription	Lung	lung
26	chr6:166742600-166754000	Weak transcription	Fetal Kidney	kidney
27	chr6:166742800-166745400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:166742800-166745800	Weak transcription	Spleen	Spleen
29	chr6:166742800-166746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:166742800-166746200	Weak transcription	Fetal Intestine Small	intestine
31	chr6:166742800-166746200	Weak transcription	Osteobl	bone
32	chr6:166742800-166746400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:166742800-166746400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:166742800-166746400	Weak transcription	Aorta	Aorta
35	chr6:166742800-166746400	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:166742800-166746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:166742800-166746800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:166742800-166747000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:166742800-166748400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:166742800-166749200	Weak transcription	NHEK	skin
41	chr6:166742800-166750000	Weak transcription	Colonic Mucosa	Colon
42	chr6:166742800-166751000	Weak transcription	HSMM	muscle
43	chr6:166743000-166745400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:166743000-166745800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:166743000-166746200	Weak transcription	Primary B cells from cord blood	blood
46	chr6:166743000-166746200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:166743000-166746200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:166743000-166746200	Weak transcription	Fetal Thymus	thymus
49	chr6:166743000-166746400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr6:166743000-166746400	Weak transcription	Thymus	Thymus

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