Variant report

Variant	rs10949374
Chromosome Location	chr6:16661992-16661993
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	chr6:16658089..16660034-chr6:16661443..16663086,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2073513	0.98[ASN][1000 genomes]
rs2073515	0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3793100	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3812194	0.81[JPT][hapmap]
rs3828864	0.95[ASN][1000 genomes]
rs719315	0.91[ASN][1000 genomes]

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	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10949374	NHLRC1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16584000-16670000	Weak transcription	Fetal Brain Male	brain
2	chr6:16636800-16667400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:16636800-16669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:16636800-16672600	Weak transcription	Gastric	stomach
5	chr6:16641800-16670400	Weak transcription	Fetal Brain Female	brain
6	chr6:16647000-16670000	Weak transcription	Pancreas	Pancrea
7	chr6:16652000-16662200	Weak transcription	Brain Germinal Matrix	brain
8	chr6:16653000-16669400	Weak transcription	Thymus	Thymus
9	chr6:16653800-16675000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:16654000-16662200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:16655800-16667800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:16656000-16667400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:16658200-16664200	Weak transcription	NHDF-Ad	bronchial
14	chr6:16658200-16667400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:16658200-16670000	Weak transcription	Left Ventricle	heart
16	chr6:16659000-16670000	Weak transcription	Ovary	ovary
17	chr6:16659200-16662000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:16659200-16667800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:16660200-16670400	Weak transcription	Fetal Lung	lung
20	chr6:16660600-16667600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:16660600-16669600	Weak transcription	Stomach Mucosa	stomach
22	chr6:16660800-16662000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:16660800-16667800	Weak transcription	Osteobl	bone
24	chr6:16660800-16669200	Weak transcription	NH-A	brain
25	chr6:16660800-16670200	Weak transcription	Liver	Liver
26	chr6:16661000-16664200	Weak transcription	Fetal Heart	heart
27	chr6:16661000-16668800	Weak transcription	Hela-S3	cervix
28	chr6:16661000-16669200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:16661200-16662400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:16661600-16662200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:16661600-16662200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
32	chr6:16661600-16662200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
33	chr6:16661600-16662200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:16661600-16662200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
35	chr6:16661600-16662200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:16661600-16662200	ZNF genes & repeats	HSMM	muscle
37	chr6:16661600-16662200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
38	chr6:16661600-16662400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:16661600-16662400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:16661600-16662400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
41	chr6:16661600-16662400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:16661600-16662400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr6:16661600-16662400	ZNF genes & repeats	HSMMtube	muscle
44	chr6:16661600-16662600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:16661600-16662600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:16661600-16662600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
47	chr6:16661600-16662600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:16661800-16662000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:16661800-16662000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
50	chr6:16661800-16662000	ZNF genes & repeats	Right Ventricle	heart

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