Variant report

Variant	rs12195744
Chromosome Location	chr6:163760582-163760583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163721882..163723526-chr6:163759692..163762187,2	K562	blood:
2	chr6:163743568..163746151-chr6:163758711..163760918,2	K562	blood:
3	chr6:163755571..163762023-chr6:163831891..163837157,6	MCF-7	breast:
4	chr6:163759847..163762654-chr6:163834528..163837162,2	MCF-7	breast:
5	chr6:163757896..163760585-chr6:163774528..163776997,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11751456	0.82[EUR][1000 genomes]
rs11752187	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11753466	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12215770	0.84[EUR][1000 genomes]
rs12215892	0.83[EUR][1000 genomes]
rs13211088	0.88[JPT][hapmap]
rs17393817	0.88[JPT][hapmap]
rs4370339	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4709711	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6925566	0.88[JPT][hapmap]
rs760887	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9458808	0.88[JPT][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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv605188	chr6:163697439-163772096	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12195744	LOC441177	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163745200-163767000	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr6:163745600-163773600	Enhancers	Brain Substantia Nigra	brain
3	chr6:163746600-163764400	Enhancers	Brain Cingulate Gyrus	brain
4	chr6:163754600-163760800	Enhancers	Fetal Muscle Leg	muscle
5	chr6:163756800-163764800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:163757400-163762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:163758000-163764200	Weak transcription	Spleen	Spleen
8	chr6:163758800-163762600	Enhancers	HSMMtube	muscle
9	chr6:163759000-163760600	Flanking Active TSS	Fetal Heart	heart
10	chr6:163759000-163760800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:163759000-163760800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:163759000-163768400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:163759200-163765200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:163759400-163760600	Enhancers	HUVEC	blood vessel
15	chr6:163759400-163760800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:163759400-163760800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr6:163759400-163762000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:163759600-163760600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:163759600-163760600	Enhancers	Fetal Stomach	stomach
20	chr6:163759600-163760800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:163759600-163763000	Enhancers	HSMM	muscle
22	chr6:163759800-163760600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:163759800-163760600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr6:163759800-163760600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:163759800-163760600	Enhancers	Fetal Kidney	kidney
26	chr6:163759800-163760800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr6:163759800-163760800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:163759800-163760800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr6:163759800-163760800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:163759800-163760800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr6:163759800-163760800	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr6:163759800-163760800	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr6:163759800-163760800	Enhancers	Fetal Lung	lung
34	chr6:163759800-163760800	Enhancers	NHDF-Ad	bronchial
35	chr6:163759800-163761000	Enhancers	Osteobl	bone
36	chr6:163760000-163760600	Enhancers	Fetal Brain Male	brain
37	chr6:163760000-163760800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:163760000-163760800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:163760200-163760600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr6:163760200-163761200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:163760200-163761400	Enhancers	Brain Germinal Matrix	brain
42	chr6:163760200-163762400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:163760200-163762400	Weak transcription	Left Ventricle	heart
44	chr6:163760200-163762400	Weak transcription	Psoas Muscle	Psoas
45	chr6:163760200-163762400	Weak transcription	Right Ventricle	heart
46	chr6:163760200-163762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:163760200-163762600	Weak transcription	Placenta	Placenta
48	chr6:163760200-163762600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr6:163760200-163763200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:163760200-163763800	Enhancers	Brain Angular Gyrus	brain

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