Variant report

Variant	rs236430
Chromosome Location	chr6:36731726-36731727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36731587..36733687-chr6:36952350..36954273,2	MCF-7	breast:
2	chr6:36724584..36727925-chr6:36730250..36733668,5	MCF-7	breast:
3	chr6:36731113..36733577-chr6:36757707..36759344,2	MCF-7	breast:
4	chr6:36726753..36730019-chr6:36730894..36734737,3	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs236422	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs236425	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs236427	0.80[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236428	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236432	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs236433	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236441	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs236478	0.82[CEU][hapmap]
rs236490	0.82[CEU][hapmap]
rs763046	0.81[CHB][hapmap]
rs86707	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380597	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv524053	chr6:36695223-36747406	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236430	ZFAND3	cis	cerebellum	SCAN
rs236430	MOCS1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36721800-36733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:36722800-36748200	Weak transcription	Fetal Kidney	kidney
3	chr6:36723800-36736200	Weak transcription	Right Atrium	heart
4	chr6:36724000-36736200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:36724800-36734400	Weak transcription	Right Ventricle	heart
6	chr6:36725600-36733800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:36725800-36735400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:36726000-36736200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:36726800-36733800	Weak transcription	Pancreas	Pancrea
10	chr6:36727000-36732000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:36727000-36732000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:36727000-36732000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:36727000-36732400	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:36727000-36733400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:36727000-36733800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:36727200-36734000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:36727200-36736400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:36727400-36735200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:36727400-36736200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:36727600-36732400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:36727600-36732800	Weak transcription	GM12878-XiMat	blood
22	chr6:36727600-36733000	Weak transcription	Colonic Mucosa	Colon
23	chr6:36728600-36732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:36728600-36732800	Weak transcription	HSMMtube	muscle
25	chr6:36729000-36732800	Weak transcription	Primary B cells from cord blood	blood
26	chr6:36729000-36732800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:36729400-36732400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:36729600-36733000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:36729600-36733000	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:36729600-36733000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:36729600-36733000	Weak transcription	Brain Substantia Nigra	brain
32	chr6:36729600-36733200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:36729600-36733200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:36729600-36733200	Weak transcription	Brain Angular Gyrus	brain
35	chr6:36729600-36733600	Weak transcription	Brain Anterior Caudate	brain
36	chr6:36729800-36733000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:36730400-36733000	Weak transcription	Spleen	Spleen
38	chr6:36730800-36733200	Weak transcription	Fetal Stomach	stomach
39	chr6:36731400-36732400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:36731400-36733200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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