Variant report

Variant	rs6508937
Chromosome Location	chr19:40843127-40843128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40842267..40845117-chr19:40949082..40951268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167565	Chromatin interaction
ENSG00000268366	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11666690	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11666860	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11667443	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11667768	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11667774	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11668006	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668520	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11669006	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11669332	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670323	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670860	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs11670912	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs11671439	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2356230	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35090721	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3730259	1.00[CHB][hapmap]
rs3760636	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs45441197	0.87[ASN][1000 genomes]
rs45497695	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803329	1.00[CHD][hapmap]
rs56672337	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59058760	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59106111	0.87[EUR][1000 genomes]
rs66623822	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67587726	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7245751	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247515	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes]
rs7249819	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252506	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73933232	0.82[EUR][1000 genomes]
rs73933236	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73933237	0.88[EUR][1000 genomes]
rs73933238	0.87[EUR][1000 genomes]
rs73933240	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73933241	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8105478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873143	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs874269	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6508937	HSD17B14	cis	parietal	SCAN
rs6508937	C19orf47	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40820800-40848400	Strong transcription	Dnd41	blood
2	chr19:40821400-40846000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:40822000-40843400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:40822000-40851000	Strong transcription	Fetal Stomach	stomach
5	chr19:40822200-40843200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:40822200-40845400	Strong transcription	Fetal Muscle Leg	muscle
7	chr19:40822400-40846200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr19:40823400-40845400	Strong transcription	Thymus	Thymus
9	chr19:40824200-40846400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:40824200-40848600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr19:40824200-40849600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr19:40825800-40845400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr19:40826400-40847400	Weak transcription	Right Atrium	heart
14	chr19:40826600-40853000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:40827600-40845000	Strong transcription	GM12878-XiMat	blood
16	chr19:40832200-40852800	Weak transcription	NHDF-Ad	bronchial
17	chr19:40833800-40846000	Weak transcription	Fetal Heart	heart
18	chr19:40834400-40853400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:40834800-40845600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:40834800-40853600	Weak transcription	Small Intestine	intestine
21	chr19:40836000-40845600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr19:40836000-40853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:40837200-40848400	Weak transcription	Psoas Muscle	Psoas
24	chr19:40837400-40847600	Weak transcription	Colonic Mucosa	Colon
25	chr19:40837400-40853400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:40837400-40853600	Weak transcription	Stomach Mucosa	stomach
27	chr19:40837600-40847400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:40837800-40846600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:40839800-40852800	Weak transcription	Hela-S3	cervix
30	chr19:40839800-40853400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:40840000-40845000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:40840000-40847400	Weak transcription	HMEC	breast
33	chr19:40840000-40852800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:40840000-40852800	Weak transcription	HUVEC	blood vessel
35	chr19:40840000-40853400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:40840000-40853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:40840200-40850400	Weak transcription	Osteobl	bone
38	chr19:40840200-40852800	Weak transcription	HepG2	liver
39	chr19:40840400-40850800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:40840400-40852800	Weak transcription	Fetal Kidney	kidney
41	chr19:40840400-40853000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:40840400-40853000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr19:40840400-40853000	Weak transcription	Fetal Brain Male	brain
44	chr19:40840400-40853400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr19:40841200-40844800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:40841400-40853000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:40841600-40847000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr19:40841800-40845600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:40842000-40843800	Enhancers	HSMM	muscle
50	chr19:40842000-40844000	Enhancers	Right Ventricle	heart

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