Variant report

Variant	rs9367924
Chromosome Location	chr6:16669367-16669368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:16647525..16649977-chr6:16668456..16671117,2	MCF-7	breast:
2	chr6:16655612..16657942-chr6:16667483..16669445,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10484365	0.92[MEX][hapmap]
rs16878738	1.00[MEX][hapmap]
rs2209026	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs59543599	0.87[ASN][1000 genomes]
rs72825589	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9350013	1.00[CHB][hapmap]
rs9370919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9396703	0.87[ASN][1000 genomes]
rs9396704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9396705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[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
rs9367924	NHLRC1	cis	parietal	SCAN

Chromatin state (count:90 , 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	chr6:16636800-16669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:16636800-16672600	Weak transcription	Gastric	stomach
4	chr6:16641800-16670400	Weak transcription	Fetal Brain Female	brain
5	chr6:16647000-16670000	Weak transcription	Pancreas	Pancrea
6	chr6:16653000-16669400	Weak transcription	Thymus	Thymus
7	chr6:16653800-16675000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:16658200-16670000	Weak transcription	Left Ventricle	heart
9	chr6:16659000-16670000	Weak transcription	Ovary	ovary
10	chr6:16660200-16670400	Weak transcription	Fetal Lung	lung
11	chr6:16660600-16669600	Weak transcription	Stomach Mucosa	stomach
12	chr6:16660800-16670200	Weak transcription	Liver	Liver
13	chr6:16662200-16669400	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:16662200-16669400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:16662200-16669400	Weak transcription	HSMM	muscle
16	chr6:16662200-16670000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:16662200-16670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:16662200-16670000	Weak transcription	Brain Anterior Caudate	brain
19	chr6:16662200-16670200	Weak transcription	Aorta	Aorta
20	chr6:16662200-16670200	Weak transcription	Esophagus	oesophagus
21	chr6:16662200-16670400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:16662200-16684000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:16662200-16684000	Weak transcription	Placenta	Placenta
24	chr6:16662200-16685200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:16662200-16699600	Weak transcription	Fetal Intestine Large	intestine
26	chr6:16662400-16669400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:16662400-16670000	Weak transcription	Psoas Muscle	Psoas
28	chr6:16662400-16699600	Weak transcription	Fetal Intestine Small	intestine
29	chr6:16662600-16669400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:16662600-16669600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:16662600-16670200	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:16663000-16669400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:16667200-16671600	Enhancers	Fetal Heart	heart
34	chr6:16667200-16672400	Enhancers	HMEC	breast
35	chr6:16667400-16670600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:16667400-16671000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:16667400-16674400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr6:16667800-16673200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:16668000-16670000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:16668200-16669400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:16668200-16669400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr6:16668200-16669400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:16668200-16669400	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:16668200-16670000	Weak transcription	Fetal Stomach	stomach
45	chr6:16668200-16670200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:16668400-16669400	Weak transcription	Adipose Nuclei	Adipose
47	chr6:16668400-16669400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr6:16668400-16669400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:16668400-16669400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:16668400-16670000	Weak transcription	Right Ventricle	heart

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