Variant report

Variant	rs12905388
Chromosome Location	chr15:83501511-83501512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83477460..83480587-chr15:83496112..83502372,6	K562	blood:
2	chr15:83495862..83497428-chr15:83499513..83501800,2	K562	blood:
3	chr15:83500530..83503230-chr15:83659180..83661791,2	K562	blood:
4	chr15:83478452..83480034-chr15:83499455..83501748,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156232	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11259951	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs11635618	1.00[CHB][hapmap]
rs11856316	0.81[CEU][hapmap];0.94[CHB][hapmap]
rs17158263	0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2046071	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs2379994	0.87[CHB][hapmap]
rs35788008	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4778691	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs7174089	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs8042254	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs9806482	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12905388	WHDC1	Cis_1M	lymphoblastoid	RTeQTL
rs12905388	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83479600-83504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:83479800-83504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:83480000-83501600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:83480400-83507000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:83481200-83507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:83481400-83507000	Strong transcription	Placenta	Placenta
7	chr15:83481600-83507000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr15:83481800-83506200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:83481800-83507000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr15:83481800-83507600	Strong transcription	Adipose Nuclei	Adipose
11	chr15:83482000-83506800	Strong transcription	Fetal Intestine Large	intestine
12	chr15:83482000-83507000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:83482200-83507000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr15:83482800-83506800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr15:83483200-83507400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:83484800-83505400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:83488400-83505000	Strong transcription	Fetal Stomach	stomach
18	chr15:83488800-83501800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr15:83489200-83506800	Weak transcription	Fetal Brain Male	brain
20	chr15:83491000-83508000	Strong transcription	Thymus	Thymus
21	chr15:83491200-83506400	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr15:83491200-83507400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:83491400-83505000	Strong transcription	Spleen	Spleen
24	chr15:83491400-83506600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:83491400-83507400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:83491400-83507400	Strong transcription	Fetal Muscle Leg	muscle
27	chr15:83491400-83508200	Strong transcription	Left Ventricle	heart
28	chr15:83491800-83506000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:83491800-83507600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:83492000-83507400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:83492200-83504200	Strong transcription	Lung	lung
32	chr15:83492200-83507400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:83492800-83506000	Strong transcription	Colonic Mucosa	Colon
34	chr15:83493000-83507600	Strong transcription	Fetal Brain Female	brain
35	chr15:83493400-83505800	Strong transcription	Dnd41	blood
36	chr15:83493600-83505600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr15:83493600-83506400	Strong transcription	Rectal Smooth Muscle	rectum
38	chr15:83493600-83507000	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr15:83493600-83507400	Strong transcription	Primary T cells from cord blood	blood
40	chr15:83493600-83507800	Strong transcription	Brain Germinal Matrix	brain
41	chr15:83493600-83508000	Strong transcription	Primary B cells from cord blood	blood
42	chr15:83494200-83502200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:83494200-83506200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:83494400-83505400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:83494800-83507400	Strong transcription	Brain Substantia Nigra	brain
46	chr15:83496400-83502400	Genic enhancers	Liver	Liver
47	chr15:83496600-83507200	Strong transcription	Colon Smooth Muscle	Colon
48	chr15:83496600-83507800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:83497400-83502000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:83497400-83506000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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