Variant report

Variant	rs41446253
Chromosome Location	chr2:38770016-38770017
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38751112..38753312-chr2:38768692..38771301,2	K562	blood:
2	chr2:38769946..38771644-chr2:38978190..38979713,2	MCF-7	breast:
3	chr2:38768041..38770034-chr2:38779562..38781817,2	K562	blood:
4	chr2:38767755..38769303-chr2:38769457..38771424,2	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1543880	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022945	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17576044	0.81[YRI][hapmap]
rs17603782	1.00[MEX][hapmap]
rs55785223	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55833813	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55957936	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56251362	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56956410	0.87[AMR][1000 genomes]
rs59114683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60475078	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6710613	0.81[YRI][hapmap]
rs6727765	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730806	0.81[YRI][hapmap]
rs6732384	0.85[AMR][1000 genomes]
rs6732743	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72895897	0.87[AMR][1000 genomes]
rs72897608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72897610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905831	0.80[AFR][1000 genomes]
rs72905837	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905839	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905843	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905844	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905847	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905860	0.94[AFR][1000 genomes]
rs72905861	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905863	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905868	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905869	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905871	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905880	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73929040	0.87[AMR][1000 genomes]
rs73929050	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73929059	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73929077	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73931606	0.85[AMR][1000 genomes]
rs7578356	1.00[MEX][hapmap]
rs7579589	0.85[AMR][1000 genomes]
rs7584862	1.00[MEX][hapmap]
rs7586241	0.87[YRI][hapmap]
rs7594264	0.85[AMR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1796304	chr2:38766721-38790750	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41446253	RNF212	trans	lymphoblastoid	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38770200	Weak transcription	HSMMtube	muscle
2	chr2:38763600-38771000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:38763800-38778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:38767400-38773400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:38767600-38770400	Enhancers	Fetal Intestine Large	intestine
7	chr2:38767800-38771200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr2:38768200-38770200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr2:38768200-38770200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr2:38768200-38770400	Enhancers	H9 Cell Line	embryonic stem cell
11	chr2:38768200-38770600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
13	chr2:38768400-38770400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:38768400-38771200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:38768800-38779000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:38769000-38770400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:38769000-38770400	Enhancers	Primary T cells from cord blood	blood
21	chr2:38769000-38771200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:38769200-38770400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:38769200-38770800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr2:38769200-38771000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr2:38769200-38776800	Weak transcription	Brain Anterior Caudate	brain
27	chr2:38769200-38782800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:38769200-38787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:38769400-38770200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:38769400-38770400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:38769600-38770400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:38769600-38770400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:38769600-38770400	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:38769600-38770400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr2:38769600-38770400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr2:38769600-38770400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:38769600-38770400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:38769600-38770400	Enhancers	Thymus	Thymus
40	chr2:38769600-38770400	Enhancers	HMEC	breast
41	chr2:38769600-38770400	Enhancers	K562	blood
42	chr2:38769600-38770400	Flanking Active TSS	NH-A	brain
43	chr2:38769600-38770600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:38769600-38770600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:38769600-38770600	Flanking Active TSS	HUVEC	blood vessel
46	chr2:38769600-38771000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:38769600-38771000	Enhancers	Fetal Thymus	thymus
48	chr2:38769600-38775600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:38769600-38777000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:38769800-38770200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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